openapi: 3.1.0
info:
title: annonars
description: Genome annotation based on Rust and RocksDB
contact:
name: Manuel Holtgrewe
email: manuel.holtgrewe@bih-charite.de
license:
name: Apache-2.0
identifier: Apache-2.0
version: 0.42.4
paths:
/api/v1/genes/clinvar:
get:
tags:
- genes_clinvar
summary: Query for ClinVar information for one or more genes.
operationId: genesClinvar
parameters:
- name: hgnc_id
in: query
description: The HGNC IDs to search for.
required: false
schema:
type:
- array
- 'null'
items:
type: string
responses:
'200':
description: Per-gene ClinVar information.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesClinvarResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/info:
get:
tags:
- genes_info
summary: Query for annotations for one or more genes.
operationId: genesInfo
parameters:
- name: hgnc_id
in: query
description: The HGNC IDs to search for.
required: false
schema:
type:
- array
- 'null'
items:
type: string
responses:
'200':
description: Per-gene information.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesInfoResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/lookup:
get:
tags:
- genes_lookup
summary: Search for genes.
operationId: genesLookup
parameters:
- name: q
in: query
description: The strings to search for.
required: true
schema:
type: array
items:
type: string
responses:
'200':
description: Genes search results.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesLookupResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/genes/search:
get:
tags:
- genes_search
summary: Search for genes.
operationId: genesSearch
parameters:
- name: q
in: query
description: The string to search for.
required: true
schema:
type: string
- name: fields
in: query
description: The fields to search in.
required: false
schema:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/GenesFields'
- name: case_sensitive
in: query
description: Enable case sensitive search.
required: false
schema:
type:
- boolean
- 'null'
responses:
'200':
description: Genes search results.
content:
application/json:
schema:
$ref: '#/components/schemas/GenesSearchResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/seqvars/annos:
get:
tags:
- annos_variant
summary: Query for annotations for a single variant.
operationId: seqvarsAnnosQuery
parameters:
- name: genome_release
in: query
description: Genome release specification.
required: true
schema:
type: string
- name: chromosome
in: query
description: Chromosome name.
required: true
schema:
type: string
- name: pos
in: query
description: 1-based position for VCF-style variant.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: reference
in: query
description: Reference allele bases.
required: true
schema:
type: string
- name: alternative
in: query
description: Alterantive allele bases.
required: true
schema:
type: string
responses:
'200':
description: Annotation for a single variant.
content:
application/json:
schema:
$ref: '#/components/schemas/SeqvarsAnnosResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/strucvars/clinvar/query:
get:
tags:
- clinvar_sv
summary: Endpoint for querying ClinVar SV annotations.
operationId: strucvarsClinvarQuery
parameters:
- name: genome_release
in: query
description: Genome release specification.
required: true
schema:
$ref: '#/components/schemas/GenomeRelease'
- name: chromosome
in: query
description: Chromosome name.
required: true
schema:
type: string
- name: start
in: query
description: 1-based start position.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: stop
in: query
description: 1-based stop postion.
required: true
schema:
type: integer
format: int32
minimum: 0
- name: variation_types
in: query
description: Optionally, the variant types.
required: false
schema:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/ClinvarExtractedVariationType'
- name: min_overlap
in: query
description: Optionally, minimal overlap.
required: false
schema:
type:
- number
- 'null'
format: double
- name: page_no
in: query
description: Optional 1-based page number.
required: false
schema:
type:
- integer
- 'null'
format: int32
minimum: 0
- name: page_size
in: query
description: Optional page size.
required: false
schema:
type:
- integer
- 'null'
format: int32
minimum: 0
responses:
'200':
description: Clinvar strucvars information.
content:
application/json:
schema:
$ref: '#/components/schemas/StrucvarsClinvarResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
/api/v1/versionsInfo:
get:
tags:
- versions
summary: Query for annotations for one variant.
operationId: versionsInfo
parameters: []
responses:
'200':
description: Version information.
content:
application/json:
schema:
$ref: '#/components/schemas/VersionsInfoResponse'
'500':
description: Internal server error.
content:
application/json:
schema:
$ref: '#/components/schemas/CustomError'
components:
schemas:
AnnoDb:
type: string
description: Encode annotation database.
enum:
- other
- cadd
- dbsnp
- dbnsfp
- dbscsnv
- gnomad_mtdna
- gnomad_exomes
- gnomad_genomes
- helixmtdb
- ucsc_conservation
- clinvar
ClinvarAccession:
type: object
description: Local type for `ClinVarAccession`
required:
- accession
- version
properties:
accession:
type: string
description: Accession.
version:
type: integer
format: int32
description: Version.
submitter_identifiers:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSubmitterIdentifiers'
description: The submitter's identifier.
date_updated:
type:
- string
- 'null'
format: date-time
description: |-
The date that the latest update to the submitted
record (SCV) became public in ClinVar.
date_created:
type:
- string
- 'null'
format: date-time
description: |-
DateCreated is the date when the record first became
public in ClinVar.
ClinvarAffectedStatus:
type: string
description: Local enumeration for the affected status.
enum:
- yes
- no
- not_provided
- unknown
- not_applicable
ClinvarAge:
type: object
description: Local type for an age.
required:
- value
- unit
- type
properties:
value:
type: integer
format: int32
description: The age value.
unit:
$ref: '#/components/schemas/ClinvarAgeUnit'
description: The age unit.
type:
$ref: '#/components/schemas/ClinvarAgeType'
description: The age type.
ClinvarAgeType:
type: string
description: Local enumeration for an age type.
enum:
- minimum
- maximum
- single
ClinvarAgeUnit:
type: string
description: Local enumeration for an age unit.
enum:
- days
- weeks
- months
- years
- weeks_gestation
- months_gestation
ClinvarAggregateClassificationSet:
type: object
description: |-
Used to bundle different types of Classifications (germline,
oncogenic, somatic clinical impact) ; Supports summary as
well as submission details.
NB: called "typeAggregateClassificationSet" in XSD.
properties:
germline_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedGermlineClassification'
description: The aggregate germline classification.
somatic_clinical_impact:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedSomaticClinicalImpact'
description: The aggregate somatic clinical impact.
oncogenicity_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregatedOncogenicityClassification'
description: The aggregate oncogenicity classification.
ClinvarAggregateGermlineReviewStatus:
type: string
description: Enumeration describing aggregate germline review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters_no_conflicts
- criteria_provided_conflicting_classifications
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregateOncogenicityReviewStatus:
type: string
description: Enumeration describing aggregate oncogenicity review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters_no_conflicts
- criteria_provided_conflicting_classifications
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregateSomaticClinicalImpactReviewStatus:
type: string
description: Enumeration describing aggregate somatic clinical impact review status value.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- criteria_provided_multiple_submitters
- reviewed_by_expert_panel
- practice_guideline
- no_classifications_from_unflagged_records
- no_classification_for_the_single_variant
ClinvarAggregatedGermlineClassification:
type: object
description: |-
Aggregated germline classification info.
Corresponds to ``typeAggregatedGermlineClassification`` in XSD.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus'
description: |-
The aggregate review status based on all germline submissions
for this record.
description:
type:
- string
- 'null'
description: |
We are not providing an enumeration for the values we report
for germline classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
explanation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: |-
Explanation is used only when the description is 'conflicting
data from submitters' The element summarizes the conflict.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAggregatedOncogenicityClassification:
type: object
description: |-
Aggregated oncogenicity classification info.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateOncogenicityReviewStatus'
description: |-
The aggregate review status based on all somatic clinical
impact submissions for this record.
description:
type:
- string
- 'null'
description: |-
We are not providing an enumeration for the values we report
for somatic clinical impact classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAggregatedSomaticClinicalImpact:
type: object
description: |-
Aggregated somatic clinical impact info.
nested elements
required:
- review_status
- xrefs
- citations
- comments
- history_records
- conditions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateSomaticClinicalImpactReviewStatus'
description: |-
The aggregate review status based on all somatic clinical
impact submissions for this record.
description:
type:
- string
- 'null'
description: |-
We are not providing an enumeration for the values we report
for somatic clinical impact classification within the xsd. Details are in
<https://github.com/ncbi/clinvar/ClassificationOnClinVar.md>
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
history_records:
type: array
items:
$ref: '#/components/schemas/ClinvarDescriptionHistory'
description: History information.
conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitSet'
description: List of conditions.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: Date of most recent submission.
number_of_submitters:
type:
- integer
- 'null'
format: int32
description: Number of submitters.
number_of_submissions:
type:
- integer
- 'null'
format: int32
description: Number of submissions.
ClinvarAllele:
type: object
description: |-
This is a record per variant (Measure/@ID,AlleleID).
Corresponds to "typeAllele" in XSD.
required:
- genes
- name
- variant_types
- locations
- other_names
- protein_changes
- hgvs_expressions
- xrefs
- comments
- functional_consequences
- allele_frequencies
- allele_id
- variation_id
properties:
genes:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleGene'
description: Gene list.
name:
type: string
description: Name.
canonical_spdi:
type:
- string
- 'null'
description: Canonical SPDI.
variant_types:
type: array
items:
type: string
description: Variant type(s).
locations:
type: array
items:
$ref: '#/components/schemas/ClinvarLocation'
description: Location.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: List of other names.
protein_changes:
type: array
items:
type: string
description: These are the single-letter representations of the protein change.
hgvs_expressions:
type: array
items:
$ref: '#/components/schemas/ClinvarHgvsExpression'
description: List of HGVS expressions.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Aggregated classifications.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: List of functional consequences.
allele_frequencies:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleFrequency'
description: Allele frequencies.
global_minor_allele_frequency:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGlobalMinorAlleleFrequency'
description: Global minor allele frequencies.
allele_id:
type: integer
format: int64
description: Allele ID.
variation_id:
type: integer
format: int64
description: Variation ID.
ClinvarAlleleDescription:
type: object
description: |-
This is to be used within co-occurrence set.
Corresponds to `typeAlleleDescr` in XSD.
required:
- name
properties:
name:
type: string
description: The name of the allele.
relative_orientation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRelativeOrientation'
description: |-
Optional relative orientation.
NB: Unused in XML
zygosity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarZygosity'
description: Optional zygosity.
clinical_significance:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarClinicalSignificance'
description: |-
Optional clinical significance.
Corresponds to `ClinicalSignificanceType` in XSD.
ClinvarAlleleFrequency:
type: object
description: Local type for allele frequency.
required:
- value
- source
properties:
value:
type: number
format: double
description: Value.
source:
type: string
description: Source.
url:
type:
- string
- 'null'
description: URL.
ClinvarAlleleGene:
type: object
description: |-
Local type for Gene.
nested elements
required:
- locations
- omims
- properties
- full_name
- gene_id
- source
properties:
locations:
type: array
items:
$ref: '#/components/schemas/ClinvarLocation'
description: Gene's locations.
omims:
type: array
items:
type: integer
format: int64
minimum: 0
description: OMIM ID.
haploinsufficiency:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarDosageSensitivity'
description: Haploinsuffiency.
triplosensitivity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarDosageSensitivity'
description: Triplosensitivity.
properties:
type: array
items:
type: string
description: |-
Used to set key words for retrieval or
display about a gene, such as genes listed by the
ACMG guidelines.
symbol:
type:
- string
- 'null'
description: Optional gene symbol.
full_name:
type: string
description: Full gene name.
gene_id:
type: integer
format: int64
description: Gene ID.
hgnc_id:
type:
- string
- 'null'
description: Optional HGNC ID.
source:
type: string
description: Source of gene (calculated or submitted).
relationship_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGeneVariantRelationship'
description: Relationship between gene and variant.
ClinvarAlleleName:
type: object
description: Local type for allele name.
required:
- value
properties:
value:
type: string
description: The name's value.
type:
type:
- string
- 'null'
description: The name's type.
ClinvarAlleleScv:
type: object
description: |-
This is a record per variant (Measure/@ID,AlleleID) as submitted for
accessioning in an SCV.
Corresponds to "typeAlleleSCV" in XSD.
required:
- genes
- other_names
- protein_changes
- xrefs
- citations
- comments
- molecular_consequences
- functional_consequences
- attributes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleScvGene'
description: |-
0 to many genes (and related data ) related to the allele
being reported.
name:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarOtherName'
description: Name provided by the submitter.
variant_type:
type:
- string
- 'null'
description: Variant type.
location:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarLocation'
description: Location.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: List of other names.
protein_changes:
type: array
items:
type: string
description: |-
Single letter representation of the amino acid change and its
location.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
molecular_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarMolecularConsequence'
description: |-
Currently redundant with the MolecularConsequence element of
the HGVS element?
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: Functional consequences.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: Attributes.
allele_id:
type:
- integer
- 'null'
format: int64
description: Allele ID.
ClinvarAlleleScvGene:
type: object
description: |-
Local type for Gene.
nested elements
required:
- properties
- xrefs
properties:
name:
type:
- string
- 'null'
description: Gene name.
properties:
type: array
items:
type: string
description: |-
Used to set key words for retrieval or
display about a gene, such as genes listed by the
ACMG guidelines.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: |-
Used for gene specific identifiers
such as MIM number, Gene ID, HGNC ID, etc.
symbol:
type:
- string
- 'null'
description: Optional gene symbol.
relationship_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGeneVariantRelationship'
description: Relationship between gene and variant.
ClinvarAssemblyStatus:
type: string
description: Local enum for the assembly status.
enum:
- current
- previous
ClinvarAssertion:
type: string
description: Enumeration describing assertion type attributes.
enum:
- variation_to_disease
- variation_to_included_disease
- variation_in_modifier_gene_to_disease
- confers_sensitivity
- confers_resistance
- variant_to_named_protein
ClinvarAttribute:
type: object
description: Extend the BaseAttribute with a `type` field.
required:
- type
properties:
base:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarBaseAttribute'
description: The base value.
type:
type: string
description: The type of the attribute.
ClinvarAttributeSetElement:
type: object
description: |-
Common type for an entry in a set of attributes.
Called ``typeAttributeSet`` in XSD.
required:
- xrefs
- citations
- comments
properties:
attribute:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAttribute'
description: The attribute value.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
ClinvarAttributeSetElementType:
type: string
description: Local enum for types.
enum:
- mode_of_inheritance
- penetrance
- age_of_onset
- severity
- classification_history
- severity_description
- assertion_method
ClinvarBaseAttribute:
type: object
description: |-
The attribute is a general element to represent a defined set of data
qualified by an enumerated set of types. For each attribute element, the value will
be a character string and is optional. Source shall be used to store identifiers for
supplied data from source other than the submitter (e.g. SequenceOntology). The data
submitted where Type="variation" shall be validated against sequence_alternation in
Sequence Ontology <http://www.sequenceontology.org/.> This is to be a generic version
of AttributeType and should be used with extension when it is used to specify Type
and its enumerations.
properties:
value:
type:
- string
- 'null'
description: The attribute's value; can be empty.
integer_value:
type:
- integer
- 'null'
format: int64
description: The optional integer value.
date_value:
type:
- string
- 'null'
format: date-time
description: The optional date value.
ClinvarChromosome:
type: string
description: Enumeration describing chromosome.
enum:
- chromosome1
- chromosome2
- chromosome3
- chromosome4
- chromosome5
- chromosome6
- chromosome7
- chromosome8
- chromosome9
- chromosome10
- chromosome11
- chromosome12
- chromosome13
- chromosome14
- chromosome15
- chromosome16
- chromosome17
- chromosome18
- chromosome19
- chromosome20
- chromosome21
- chromosome22
- x
- y
- mt
- par
- un
ClinvarCitation:
type: object
description: Description of a citation.
required:
- ids
properties:
ids:
type: array
items:
$ref: '#/components/schemas/ClinvarIdType'
description: Optional list of IDs.
url:
type:
- string
- 'null'
description: Optional URL.
citation_text:
type:
- string
- 'null'
description: Optional citation text.
type:
type:
- string
- 'null'
description: |-
This maintained distinct from publication types in PubMed and
established by GTR curators. The default is 'general'.
abbrev:
type:
- string
- 'null'
description: Corresponds to the abbreviation reported by GTR.
ClinvarClassificationScore:
type: object
description: Classification score description.
required:
- value
properties:
value:
type: number
format: double
description: The score's value.
type:
type:
- string
- 'null'
description: The score's type; optional.
ClinvarClassificationScv:
type: object
description: |-
Report classification of a variant for a SCV.
Corresponds to `ClassificationTypeSCV` in XSD.
required:
- review_status
- classification_scores
- xrefs
- citations
- comments
properties:
review_status:
$ref: '#/components/schemas/ClinvarSubmitterReviewStatus'
description: The field's review status.
germline_classification:
type:
- string
- 'null'
description: |-
The germline classification; mutually exlusive with `somatic_clinical_impact`
and `oncogenicity_classification`.
somatic_clinical_impact:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarClassificationScvSomaticClinicalImpact'
description: |-
Information on the clinical impact; mutually exlusive with `germline_classification`
and `oncogenicity_classification`.
oncogenicity_classification:
type:
- string
- 'null'
description: |-
The oncogenicity classification; mutually exlusive with `germline_classification`
and `oncogenicity_classification`.
explanation_of_classification:
type:
- string
- 'null'
description: Optional explanation of classification.
classification_scores:
type: array
items:
$ref: '#/components/schemas/ClinvarClassificationScore'
description: List of classification scores.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
ClinvarClassificationScvSomaticClinicalImpact:
type: object
description: Clinical impact of a somatic variatn.
required:
- value
properties:
value:
type: string
description: The somatic clinical impact value.
clinical_impact_assertion_type:
type:
- string
- 'null'
description: Type of the clinical impact assertion.
clinical_impact_clinical_significance:
type:
- string
- 'null'
description: Clinical impact significance.
drug_for_therapeutic_assertion:
type:
- string
- 'null'
description: Name of the drug for the therapeutic assertion.
ClinvarClassifiedCondition:
type: object
description: |-
Interpreted condition for an RCV record.
Corresponds to `typeRCVInterpretedCondition` in XSD.
required:
- value
properties:
value:
type: string
description: Condition value.
db:
type:
- string
- 'null'
description: Database name.
id:
type:
- string
- 'null'
description: Identifier in database.
ClinvarClassifiedRecord:
type: object
description: |-
This element is restricted to variation records for which an explicit
classification was submitted. Compare to IncludedRecord, which provides aggregate
information about variants that are part of another submission, but for which
ClinVar has *not* received a submission specific to that variant independently.
required:
- clinical_assertions
- trait_mappings
- deleted_scvs
- general_citations
properties:
simple_allele:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAllele'
description: |-
Describes a single sequence change relative to a
contiguous region of a chromosome or the mitochondrion.
Mutually exclusive with `haplotype` and `genotype`.
haplotype:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarHaplotype'
description: |-
Describes multiple sequence changes on one of the
chromosomes of a homologous pair or on the mitochondrion.
Mutually exclusive with `simple_allele` and `genotype`.
genotype:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGenotype'
description: |-
Describes the combination of sequence changes on each
chromosome of a homologous pair.
Mutually exclusive with `simple_allele` and `haplotype`.
rcv_list:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvList'
description: List of RCV records.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: List of classifications.
clinical_assertions:
type: array
items:
$ref: '#/components/schemas/ClinvarClinicalAssertion'
description: List of clinical assertions.
trait_mappings:
type: array
items:
$ref: '#/components/schemas/ClinvarRcvTraitMapping'
description: |-
This element is used to report how each user-submitted
trait name was mapped to a MedGen CUI identifier and a preferred name.
The structure may be used in the future to report, when a trait is
identified by a source's identifier (e.g. MIM number), the preferred
name used by that source at the time of submission. For MappingType
XRef, MappingRef is the database name and MappingValue is the database's
identifier. For MappingType Name, MappingRef is Alternate or Preferred,
and MappingValue is the submitted name of the trait. ClinicalAssertionID
is an integer identifier that corresponds 1:1 to the SCV assigned to the
submission.
deleted_scvs:
type: array
items:
$ref: '#/components/schemas/ClinvarDeletedScv'
description: List of deleted SCVs.
general_citations:
type: array
items:
$ref: '#/components/schemas/ClinvarGeneralCitations'
description: List of general citations.
ClinvarClassifiedVariation:
type: object
description: Local type for tag `ClassifiedVariation`.
required:
- variation_id
- version
properties:
variation_id:
type: integer
format: int64
description: Variation ID.
accession:
type:
- string
- 'null'
description: Optional accession.
version:
type: integer
format: int32
description: Version.
ClinvarClinicalAssertion:
type: object
description: |-
A clinical assertion as submitted (SCV record).
Corresponds to `MeasureTraitType` in XSD and `<ClinicalAssertion>` in XML
required:
- additional_submitters
- record_status
- replaces
- replaceds
- assertion
- attributes
- observed_ins
- citations
- comments
- submission_names
properties:
clinvar_submission_id:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSubmissionId'
description: The ClinVar submission ID.
clinvar_accession:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAccession'
description: The ClinVar SCV accessions.
additional_submitters:
type: array
items:
$ref: '#/components/schemas/ClinvarSubmitter'
description: Optional list of additional submitters.
record_status:
$ref: '#/components/schemas/ClinvarClinicalAssertionRecordStatus'
description: Record status.
replaces:
type: array
items:
type: string
description: Replaces; mutually exclusive with replaceds
replaceds:
type: array
items:
$ref: '#/components/schemas/ClinvarClinicalAssertionRecordHistory'
description: Replaced list; mutually exclusive with replaces
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarClassificationScv'
description: SCV classification.
assertion:
$ref: '#/components/schemas/ClinvarAssertion'
description: The assertion.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarClinicalAssertionAttributeSetElement'
description: Attributes.
observed_ins:
type: array
items:
$ref: '#/components/schemas/ClinvarObservedIn'
description: Observed in.
simple_allele:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAlleleScv'
description: Allele in SCV; mutually exclusive with haplotype/genotype.
haplotype:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarHaplotypeScv'
description: Haplotype in SCV; mutually exclusive with allele/genotype.
genotype:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGenotypeScv'
description: Genotype in SCV; mutually exclusive with allele/haplotype.
trait_set:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarTraitSet'
description: The trait set.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
study_name:
type:
- string
- 'null'
description: Optional study name.
study_description:
type:
- string
- 'null'
description: Optional study description.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
submission_names:
type: array
items:
type: string
description: List of submissions.
date_created:
type:
- string
- 'null'
format: date-time
description: Date of creation.
date_last_updated:
type:
- string
- 'null'
format: date-time
description: Date of creation.
submission_date:
type:
- string
- 'null'
format: date-time
description: Date of creation.
id:
type:
- integer
- 'null'
format: int64
description: ID.
minimum: 0
fda_recognized_database:
type:
- boolean
- 'null'
description: Whether it is an FDA recognized database.
ClinvarClinicalAssertionAttributeSetElement:
type: object
description: Local type for attribute set.
required:
- type
- xrefs
- citations
- comments
properties:
attribute:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarBaseAttribute'
description: The base value.
type:
$ref: '#/components/schemas/ClinvarAttributeSetElementType'
description: The type of the attribute.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
ClinvarClinicalAssertionRecordHistory:
type: object
description: |-
Inside ClinicalAssertion, a structure to support reporting of an
accession, its version, the date its status changed, and text describing that
change.
Corresponds to `typeClinicalAssertionRecordHistory` in XSD.
required:
- accession
properties:
comment:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: Optional comment.
accession:
type: string
description: Accession.
version:
type:
- integer
- 'null'
format: int32
description: Optional version.
date_changed:
type:
- string
- 'null'
format: date-time
description: Date of the record.
ClinvarClinicalAssertionRecordStatus:
type: string
description: Local enum for record status.
enum:
- current
- replaced
- removed
ClinvarClinicalFeaturesAffectedStatusType:
type: string
description: Enumeration describing clinical features affected status.
enum:
- present
- absent
- not_tested
ClinvarClinicalSignificance:
type: object
description: |-
Describes the clinical significance of a variant.
Corresponds to `ClinicalSignificanceType` in XSD.
contained elements
required:
- xrefs
- citations
- comments
properties:
review_status:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSubmitterReviewStatus'
description: The optional review status.
description:
type:
- string
- 'null'
description: |-
Structure used to support old data of AlleleDescriptionSet
within Co-occurenceSet.
NB: unused in XML
explanation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: |-
Optional explanatory comment.
Explanation is used only when the description is 'conflicting
data from submitters' The element summarizes the conflict.
NB: unused in XML
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Optional list of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Optional list of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Optional list of comments.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: |-
Date of last evaluation.
NB: unused in XML
ClinvarComment:
type: object
description: |-
A structure to support reporting unformatted content, with type and
source specified.
required:
- value
properties:
value:
type: string
description: The comment's value.
data_source:
type:
- string
- 'null'
description: The optional comment data source.
type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarCommentType'
description: The comment's type.
ClinvarCommentType:
type: string
description: Enumeration describing comment type.
enum:
- public
- converted_by_ncb
- missing_from_assembly
- genomic_location_not_established
- location_on_genome_and_product_not_aligned
- deletion_comment
- merge_comment
- assembly_specific_allele_definition
- alignment_gap_makes_appear_inconsistent
- explanation_of_classification
- flagged_comment
ClinvarCooccurrence:
type: object
description: This refers to the zygosity of the variant being asserted.
required:
- allele_descriptions
properties:
zygosity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarZygosity'
description: Optional zygosity.
allele_descriptions:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleDescription'
description: The allele descriptions.
count:
type:
- integer
- 'null'
format: int32
description: The optional count.
ClinvarDeletedScv:
type: object
description: |-
A structure to support reporting of an accession, its version, the
date it was deleted and a free-text summary of why it was deleted.
Corresponds to `typeDeletedSCV`.
required:
- accession
- version
properties:
accession:
type: string
description: The accession.
version:
type: integer
format: int32
description: The version.
date_deleted:
type:
- string
- 'null'
format: date-time
description: The date of deletion.
ClinvarDescriptionHistory:
type: object
description: |-
Description of the history of a record.
Called ``typeDescriptionHistory`` in XSD.
required:
- description
properties:
description:
type: string
description: The pathogenicity description.
dated:
type:
- string
- 'null'
format: date-time
description: The date of the description.
ClinvarDosageSensitivity:
type: object
description: |-
Haploinsufficiency/Triplosensitivity of gene.
nested elements
required:
- value
properties:
value:
type: string
description: Value.
last_evaluated:
type:
- string
- 'null'
format: date-time
description: Optional last evaluated date.
clingen:
type:
- string
- 'null'
description: URL to ClinGen.
ClinvarEvidenceType:
type: string
description: |-
Enumeration describing evidence type.
Corresponds to "EvidenceType" in XSD.
enum:
- genetic
- experimental
- population
- computational
ClinvarExtractedRcvRecord:
type: object
description: Protocol buffer for storing essential information of one RCV.
required:
- title
properties:
accession:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarVersionedAccession'
description: The accession.
title:
type: string
description: Title of RCV.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvClassifications'
description: Classifications (thinned out).
ClinvarExtractedVariationType:
type: string
description: Enumeration for the type of the variant.
enum:
- insertion
- deletion
- snv
- indel
- duplication
- tandem_duplication
- structural_variant
- copy_number_gain
- copy_number_loss
- protein_only
- microsatellite
- inversion
- other
ClinvarExtractedVcvRecord:
type: object
description: Protocol buffer for storing essential information of one VCV.
required:
- rcvs
- name
- variation_type
- clinical_assertions
- hgnc_ids
properties:
accession:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarVersionedAccession'
description: The accession.
rcvs:
type: array
items:
$ref: '#/components/schemas/ClinvarExtractedRcvRecord'
description: List of aggregated RCVs.
name:
type: string
description: Name of VCV.
variation_type:
$ref: '#/components/schemas/ClinvarExtractedVariationType'
description: The type of the variant.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Classifications (thinned out).
clinical_assertions:
type: array
items:
$ref: '#/components/schemas/ClinvarClinicalAssertion'
description: Clinical assertions (thinned out),
sequence_location:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSequenceLocation'
description: The sequence location on one reference.
hgnc_ids:
type: array
items:
type: string
description: List of HGNC IDs.
ClinvarFamilyData:
type: object
description: |-
Structure to describe attributes of any family data in an observation.
If the details of the number of families and the de-identified pedigree id are not
available, use FamilyHistory to describe what type of family data is available. Can
also be used to report 'Yes' or 'No' if there are no more details.
Corresponds to "FamilyInfo" in XSD.
nested elements
properties:
family_history:
type:
- string
- 'null'
description: Optional family history.
num_families:
type:
- integer
- 'null'
format: int32
description: Number of families.
num_families_with_variant:
type:
- integer
- 'null'
format: int32
description: Number of families with variant.
num_families_with_segregation_observed:
type:
- integer
- 'null'
format: int32
description: Number of families with segregation observed.
pedigree_id:
type:
- string
- 'null'
description: Pedigree ID.
segregation_observed:
type:
- string
- 'null'
description: Segregation oberved (yes, no, number)
ClinvarFunctionalConsequence:
type: object
description: |-
Description of a functional consequence.
Corresponds to `typeFunctionalConsequence` in XSD.
nested elements
required:
- xrefs
- citations
- comments
- value
properties:
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
value:
type: string
description: Value of functional consequence.
ClinvarGender:
type: string
description: Local enumeration for gender.
enum:
- male
- female
- mixed
ClinvarGeneVariantRelationship:
type: string
description: |-
Enumeration describing connection between genes and variants.
Corresponds to XSD type "GeneVariantRelationship".
enum:
- variant_within_gene
- gene_overlapped_by_variant
- near_gene_upstream
- near_gene_downstream
- asserted_but_not_computed
- within_multiple_genes_by_overlap
- within_single_gene
ClinvarGeneralCitations:
type: object
description: Type for the tag `GeneralCitations`.
required:
- xrefs
- citations
properties:
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
ClinvarGenericSetElement:
type: object
description: |-
Entry in an element set.
Called ``SetElementSetType`` in XSD.
required:
- value
- type
- citations
- xrefs
- comments
properties:
value:
type: string
description: The element's value.
type:
type: string
description: The element's type.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
ClinvarGenotype:
type: object
description: |-
Used to report genotypes, be they simple or complex diplotypes.
Corresponds to "typeGenotype" in XSD.
nested elements
required:
- simple_alleles
- haplotypes
- name
- variation_type
- other_names
- hgvs_expressions
- functional_consequences
- xrefs
- citations
- comments
- attributes
properties:
simple_alleles:
type: array
items:
$ref: '#/components/schemas/ClinvarAllele'
description: Simple allele; mutually exclusive with `haplotype`.
haplotypes:
type: array
items:
$ref: '#/components/schemas/ClinvarHaplotype'
description: |-
Haplotype; mutually exclusive with `simple_allele`.
Allows more than 2 haplotypes per genotype to support
representation of ploidy.
name:
type: string
description: Optional name.
variation_type:
$ref: '#/components/schemas/ClinvarVariationType'
description: The variation type.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: Names other than 'preferred' used for the Genotype.
hgvs_expressions:
type: array
items:
$ref: '#/components/schemas/ClinvarHgvsExpression'
description: HGVS descriptions.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: Functional consequences.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Aggregated classifications.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: Attributes.
variation_id:
type:
- integer
- 'null'
format: int64
description: Variation ID.
ClinvarGenotypeScv:
type: object
description: |-
Used to report genotypes, be they simple or complex diplotypes.
Corresponds to "typeGenotypeSCV" in XSD.
nested elements
required:
- simple_alleles
- haplotypes
- other_names
- variation_type
- functional_consequences
- attributes
- citations
- xrefs
- comments
properties:
simple_alleles:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleScv'
description: Simple alleles; mutually exclusive with `haplotypes`.
haplotypes:
type: array
items:
$ref: '#/components/schemas/ClinvarHaplotypeScv'
description: |-
Haplotype; mutually exclusive with `simple_alleles`.
Allows more than 2 haplotypes per genotype to support
representation of ploidy.
name:
type:
- string
- 'null'
description: Optional name.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: Other names used for the genotype.
variation_type:
$ref: '#/components/schemas/ClinvarVariationType'
description: The variation type.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: Functional consequences.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: Attributes.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
variation_id:
type:
- integer
- 'null'
format: int64
description: Variation ID.
ClinvarGlobalMinorAlleleFrequency:
type: object
description: Local type for GlobalMinorAlleleFrequency.
required:
- value
- source
properties:
value:
type: number
format: double
description: Value.
source:
type: string
description: Source.
minor_allele:
type:
- string
- 'null'
description: Minor allele.
url:
type:
- string
- 'null'
description: URL.
ClinvarHaploVariationType:
type: string
description: Enumeration describing haplotype variation types.
enum:
- haplotype
- haplotype_single_variant
- variation
- phase_unknown
- haplotype_defined_by_single_variant
ClinvarHaplotype:
type: object
description: |-
This is a record of one or more simple alleles on the same chromosome
molecule.
Corresponds to `typeHaplotype` in XSD
required:
- simple_alleles
- name
- variation_type
- other_names
- hgvs_expressions
- functional_consequences
- xrefs
- comments
- variation_id
properties:
simple_alleles:
type: array
items:
$ref: '#/components/schemas/ClinvarAllele'
description: The list of alleles in the haplotype.
name:
type: string
description: The preferred representation of the haplotype.
variation_type:
$ref: '#/components/schemas/ClinvarVariationType'
description: The type of the haplotype.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: Names other than 'preferred' used for the haplotype.
hgvs_expressions:
type: array
items:
$ref: '#/components/schemas/ClinvarHgvsExpression'
description: |-
List of all the HGVS expressions valid for, or used to submit,
a variant.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Classifications of the variant.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: Functional consequences of the variant.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of cross-references.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
variation_id:
type: integer
format: int64
description: Variation ID.
number_of_copies:
type:
- integer
- 'null'
format: int32
description: Number of copies.
number_of_chromosomes:
type:
- integer
- 'null'
format: int32
description: Number of chromosomes.
ClinvarHaplotypeScv:
type: object
description: |-
This is a record of a haplotype in SCV.
Corresponds to `typeHaplotypeSCV` in XSD.
required:
- simple_alleles
- other_names
- functional_consequences
- attributes
- citations
- xrefs
- comments
properties:
simple_alleles:
type: array
items:
$ref: '#/components/schemas/ClinvarAlleleScv'
description: The list of alleles in the haplotype.
name:
type:
- string
- 'null'
description: The preferred representation of the haplotype.
other_names:
type: array
items:
$ref: '#/components/schemas/ClinvarOtherName'
description: Names other than 'preferred' used for the haplotype.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Classification of the variant.
functional_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarFunctionalConsequence'
description: Functional consequences of the variant.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: List of attributes.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of cross-references.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
variation_id:
type:
- integer
- 'null'
format: int64
description: Variation ID.
number_of_copies:
type:
- integer
- 'null'
format: int32
description: Number of copies.
number_of_chromosomes:
type:
- integer
- 'null'
format: int32
description: Number of chromosomes.
ClinvarHgvsExpression:
type: object
description: |-
A structure to represent an HGVS expression for a nucleotide sequence
variant, along with the predicted protein change and the predicted molecular
consequence. Also used to represent only the protein change if that is all that has
been reported.
Corresponds to `typeHVSExpression` in XSD.
nested elements
required:
- molecular_consequences
- type
properties:
nucleotide_expression:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarHgvsNucleotideExpression'
description: Optional nucleotide sequence expression.
protein_expression:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarHgvsProteinExpression'
description: Optional protein sequence expression.
molecular_consequences:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of molecular consequences.
type:
$ref: '#/components/schemas/ClinvarHgvsType'
description: Type of HGVS expression.
assembly:
type:
- string
- 'null'
description: Optional assembly.
ClinvarHgvsNucleotideExpression:
type: object
description: |-
Description of a nucleotide sequence expression.
Corresponds to `typeNucleotideSequenceExpression`
required:
- expression
properties:
expression:
type: string
description: The expression values.
sequence_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarNucleotideSequence'
description: The type of the nucleotide sequence.
sequence_accession_version:
type:
- string
- 'null'
description: Optional sequence accession version.
sequence_accession:
type:
- string
- 'null'
description: Optional sequence accession.
sequence_version:
type:
- integer
- 'null'
format: int32
description: Optional sequence version.
change:
type:
- string
- 'null'
description: Optional description of the change.
assembly:
type:
- string
- 'null'
description: Optional assembly information.
submitted:
type:
- string
- 'null'
description: Optional submission information.
mane_select:
type:
- boolean
- 'null'
description: Optional MANE Select flag.
mane_plus_clinical:
type:
- boolean
- 'null'
description: Optional MANE Plus Clinical flag.
ClinvarHgvsProteinExpression:
type: object
description: |-
Description of a protein sequence expression.
Corresponds to `typeProteinSequenceExpression` in XSD.
required:
- expression
properties:
expression:
type: string
description: The expression values.
sequence_accession_version:
type:
- string
- 'null'
description: Optional sequence accession version.
sequence_accession:
type:
- string
- 'null'
description: Optional sequence accession.
sequence_version:
type:
- integer
- 'null'
format: int32
description: Optional sequence version.
change:
type:
- string
- 'null'
description: Optional description of the change.
ClinvarHgvsType:
type: string
description: Enumeration describing HGVS types.
enum:
- coding
- genomic
- genomic_top_level
- non_coding
- protein
ClinvarIdType:
type: object
description: Local ID with source.
required:
- value
- source
properties:
value:
type: string
description: The citation's value.
source:
type: string
description: If there is an identifier, what database provides it.
ClinvarIncludedRecord:
type: object
description: |-
This element is used for alleles that were not directly part of a
submission but were part of a complex submission. They have no direct submitted
classification, but are being reported for a complete representation of all alleles
in ClinVar. Compare to ClassifiedRecord.
required:
- submitted_classifications
- classified_variations
- general_citations
properties:
simple_allele:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAllele'
description: Simple allele; mutually exclusive with haplotype.
haplotype:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarHaplotype'
description: Haplotype; mutually exclusive with simple_allele.
classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAggregateClassificationSet'
description: Aggregate classification sets.
submitted_classifications:
type: array
items:
$ref: '#/components/schemas/ClinvarScv'
description: List of submitted records.
classified_variations:
type: array
items:
$ref: '#/components/schemas/ClinvarClassifiedVariation'
description: |-
Maintains the list of classified variants represented in
this submission, although not submitted with an Classification
independently.
general_citations:
type: array
items:
$ref: '#/components/schemas/ClinvarGeneralCitations'
description: List of general citations.
ClinvarIndication:
type: object
description: |-
Describes an indication.
NB: Called "IndicationType" in the XSD.
required:
- traits
- names
- attributes
- xrefs
- citations
- comments
- type
properties:
traits:
type: array
items:
$ref: '#/components/schemas/ClinvarTrait'
description: Represents the value for the test indication as a name of a trait.
names:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: List of names.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: List of attributes.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
type:
$ref: '#/components/schemas/ClinvarIndicationType'
description: The type of indication.
ClinvarIndicationType:
type: string
description: Enumeration for the indication type.
enum:
- indication
ClinvarLocation:
type: object
description: |-
There can be multiple types of location, and the locations may have
identifiers in other databases.
Corresponds to `typeLocation` in XSD.
required:
- cytogenetic_locations
- sequence_locations
- gene_locations
- xrefs
properties:
cytogenetic_locations:
type: array
items:
type: string
description: |-
Cytogenetic location is maintained independent of sequence
location, and can be submitted or computed from the sequence location.
Between 0 and 4 entries.
sequence_locations:
type: array
items:
$ref: '#/components/schemas/ClinvarSequenceLocation'
description: |-
Location on a defined sequence, with reference and alternate
allele, and start /stop values depending on the specificity with which the
variant location is known. The number system of offset 1, and
right-justified to be consistent with HGVS location data.
gene_locations:
type: array
items:
type: string
description: The location of the variant relative to features within the gene.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
ClinvarMethod:
type: object
description: |-
Details of a method used to generate variant calls or predict/report
functional consequence. The name of the platform should represent a sequencer or an
array, e.g. sequencing or array , e.g. capillary, 454, Helicos, Solexa, SOLiD. This
structure should also be used if the method is 'Curation'.
Corresponds to `MethodType` in XSD.
required:
- citations
- xrefs
- software
- method_type
- method_attributes
- obs_method_attributes
properties:
name_platform:
type:
- string
- 'null'
description: Platform name.
type_platform:
type:
- string
- 'null'
description: Platform type.
purpose:
type:
- string
- 'null'
description: Method purpose.
result_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarResultType'
description: Method result type.
min_reported:
type:
- string
- 'null'
description: Smallest reported.
max_reported:
type:
- string
- 'null'
description: Largest reported.
reference_standard:
type:
- string
- 'null'
description: Reference standard.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
description:
type:
- string
- 'null'
description: |-
Free text to enrich the description of the method and to
provide information not captured in specific fields.
software:
type: array
items:
$ref: '#/components/schemas/ClinvarSoftware'
description: List of softwares used.
source_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarMethodSourceType'
description: Source type.
method_type:
$ref: '#/components/schemas/ClinvarMethodListType'
description: Method type.
method_attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarMethodAttribute'
description: Method attribute.
obs_method_attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarObsMethodAttribute'
description: |-
ObsMethodAttribute is used to indicate an attribute specific
to a particular method in conjunction with a particular observation .
ClinvarMethodAttribute:
type: object
description: Local type for method attribute.
required:
- type
properties:
base:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarBaseAttribute'
description: The base value.
type:
$ref: '#/components/schemas/ClinvarMethodAttributeType'
description: The attribute type.
ClinvarMethodAttributeType:
type: string
description: Local enumeration of attribute type.
enum:
- location
- controls_appropriate
- method_appropriate
- test_name
- struct_var_method_type
- probe_accession
ClinvarMethodListType:
type: string
description: |-
Enumeration describing method list.
Corresponds to "MethodListType" in XSD.
enum:
- literature_only
- reference_population
- case_control
- clinical_testing
- in_vitro
- in_vivo
- research
- curation
- not_provided
- provider_interpretation
- phenotyping_only
ClinvarMethodSourceType:
type: string
description: Local enumeration for SourceType.
enum:
- submitter_generated
- data_mining
- data_review
ClinvarMethodType:
type: string
description: Local enum for the method type.
enum:
- literature_only
- reference_population
- case_control
- clinical_testing
- in_vitro
- in_vivo
- inferred_from_source
- research
ClinvarMolecularConsequence:
type: object
description: |-
Local type for MolecularConsequence.
nested elements
required:
- xrefs
- citations
- comments
- function
properties:
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Xref list.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Citation list.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Comment list.
rs:
type:
- integer
- 'null'
format: int64
description: RS id.
hgvs:
type:
- string
- 'null'
description: Optional HGVS expression.
so_id:
type:
- string
- 'null'
description: Optional SO id.
function:
type: string
description: Function.
ClinvarNucleotideSequence:
type: string
description: Enumeration describing nucleotide sequence.
enum:
- genomic_top_level
- genomic_ref_seq_gene
- genomic
- coding
- non_coding
- protein
ClinvarObsMethodAttribute:
type: object
description: Local type for observation method attribute.
required:
- type
- comments
properties:
base:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarBaseAttribute'
description: The base value.
type:
$ref: '#/components/schemas/ClinvarObsMethodAttributeType'
description: The attribute type.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Optional comments.
ClinvarObsMethodAttributeType:
type: string
description: Local enumeration for attribute type.
enum:
- method_result
- testing_laboratory
ClinvarObservedData:
type: object
description: |-
This is an AttributeSet, there will be 1 attribute supported
by optional citations, xrefs and comment. There must be at least one
ObservedData Set, but can be any number. For each ObservedData set the
Attribute will be either decimal or string depending on type. The value will
be stored here, but decimals will be entered to the database as a string.
required:
- attributes
- citations
- xrefs
- comments
properties:
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarObservedDataAttribute'
description: Attributes.
severity:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSeverity'
description: Severity.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Citation list.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Xref list.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Comment list.
ClinvarObservedDataAttribute:
type: object
description: Local struct for attributes based on `BaseAttribute`.
required:
- type
properties:
base:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarBaseAttribute'
description: base
type:
$ref: '#/components/schemas/ClinvarObservedDataAttributeType'
description: type
ClinvarObservedDataAttributeType:
type: string
description: Local enum for the observed data type.
enum:
- description
- variant_alleles
- subjects_with_variant
- subjects_with_different_causative_variant
- variant_chromosomes
- independent_observations
- single_heterozygous
- compound_heterozygous
- homozygous
- hemizygous
- number_mosaic
- observed_unspecified
- allele_frequency
- secondary_finding
- genotype_and_moi_consistent
- unaffected_family_member_with_causative_variant
- het_parent_transmit_normal_allele
- cosegregating_families
- informative_meioses
- sample_local_id
- sample_variant_id
- family_history
- num_families_with_variant
- num_families_with_segregation_observed
- segregation_observed
ClinvarObservedIn:
type: object
description: |-
Documents in what populations or samples an allele or genotype has
been observed relative to the described trait. Summary observations can be
registered per submitted assertion, grouped by common citation, study type, origin,
ethnicity, tissue, cell line, and species data. Not all options are valid per study
type, but these will not be validated in the xsd.
Corresponds to `ObservationSet` in XSD.
required:
- observed_data
- cooccurrence_sets
- citations
- xrefs
- comments
properties:
sample:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSample'
description: Sample.
observed_data:
type: array
items:
$ref: '#/components/schemas/ClinvarObservedData'
description: Observed data.
cooccurrence_sets:
type: array
items:
$ref: '#/components/schemas/ClinvarCooccurrence'
description: Co-occurence set.
trait_set:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarTraitSet'
description: TraitSet.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Citation list.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Xref list.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Comment list.
ClinvarOrigin:
type: string
description: Enumeration describing origin.
enum:
- germline
- somatic
- de_novo
- not_provided
- inherited
- maternal
- paternal
- uniparental
- biparental
- not_reported
- tested_inconclusive
- unknown
- not_applicable
- experimentally_generated
ClinvarOtherName:
type: object
description: |-
A name with an optional type.
Corresponds to `typeNames` in XSD.
required:
- value
properties:
value:
type: string
description: The name's value.
type:
type:
- string
- 'null'
description: The name's type.
ClinvarPhenotypeSetType:
type: string
description: Enumeration describing phenotype set.
enum:
- disease
- drug_response
- finding
- phenotype_instruction
- trait_choice
ClinvarProteinSequence:
type: string
description: Enumeration describing protein sequence.
enum:
- protein
ClinvarRcvAccession:
type: object
description: Corresponds to "typeRCV" in XSD.
required:
- replaceds
- accession
- version
properties:
classified_condition_list:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvClassifiedConditionList'
description: The list of classified conditions.
rcv_classifications:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvClassifications'
description: The list of RCV classifications.
replaceds:
type: array
items:
$ref: '#/components/schemas/ClinvarRecordHistory'
description: The list of RCV accessions this record has replaced.
title:
type:
- string
- 'null'
description: Optional title.
accession:
type: string
description: Accession.
version:
type: integer
format: int32
description: Version.
ClinvarRcvAccessionSomaticClinicalImpact:
type: object
description: |-
Local type for SomaticClinicalImpact.
The aggregate review status based on
all somatic clinical impact submissions for this
record.
required:
- review_status
- descriptions
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateSomaticClinicalImpactReviewStatus'
description: |-
The aggregate review status based on
all somatic clinical impact submissions for this
record.
descriptions:
type: array
items:
$ref: '#/components/schemas/ClinvarRcvSomaticClinicalImpactDescription'
description: The oncogenicity description.
ClinvarRcvClassifications:
type: object
description: Local type for RCV classifications.
properties:
germline_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvGermlineClassification'
description: Germline classification.
somatic_clinical_impact:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvAccessionSomaticClinicalImpact'
description: Somatic clinical impact.
oncogenicity_classification:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvOncogenicityClassification'
description: Oncogenicity classification.
ClinvarRcvClassifiedConditionList:
type: object
description: |-
Local type for ClassifiedConditionList.
nested elements
required:
- classified_conditions
properties:
classified_conditions:
type: array
items:
$ref: '#/components/schemas/ClinvarClassifiedCondition'
description: List of interpreted conditions.
trait_set_id:
type:
- integer
- 'null'
format: int64
description: Trait set ID.
ClinvarRcvGermlineClassification:
type: object
description: |-
Local type for GermlineClassification.
The aggregate review status based on
all germline submissions for this record.
required:
- review_status
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus'
description: |-
The aggregate review status based on
all somatic clinical impact submissions for this
record.
description:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvGermlineClassificationDescription'
description: The oncogenicity description.
ClinvarRcvGermlineClassificationDescription:
type: object
description: Local type for Description.
required:
- value
properties:
value:
type: string
description: The description.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: The date of the description.
submission_count:
type:
- integer
- 'null'
format: int32
description: The number of submissions.
minimum: 0
ClinvarRcvList:
type: object
description: Local type for tag `RCVList`.
required:
- rcv_accessions
properties:
rcv_accessions:
type: array
items:
$ref: '#/components/schemas/ClinvarRcvAccession'
description: The RCV record.
submission_count:
type:
- integer
- 'null'
format: int32
description: The number of submissions (SCV accessions) referencing the VariationID.
independent_observations:
type:
- integer
- 'null'
format: int32
description: The number of idependent observations.
ClinvarRcvOncogenicityClassification:
type: object
description: Local type for OncogenicityClassification.
required:
- review_status
properties:
review_status:
$ref: '#/components/schemas/ClinvarAggregateGermlineReviewStatus'
description: |-
The aggregate review status based on
all oncogenic submissions for this record.
description:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRcvOncogenicityDescription'
description: The oncogenicity description.
ClinvarRcvOncogenicityDescription:
type: object
description: Local type for Description.
required:
- value
properties:
value:
type: string
description: The description.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: The date of the description.
submission_count:
type:
- integer
- 'null'
format: int32
description: The number of submissions.
minimum: 0
ClinvarRcvSomaticClinicalImpactDescription:
type: object
description: Local type for Description.
required:
- value
properties:
value:
type: string
description: The description.
clinical_impact_assertion_type:
type:
- string
- 'null'
description: Clinical impact assertion type.
clinical_impact_clinical_significance:
type:
- string
- 'null'
description: Clinical impact significance
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: The date of the description.
submission_count:
type:
- integer
- 'null'
format: int32
description: The number of submissions.
minimum: 0
ClinvarRcvTraitMapping:
type: object
description: Local type for the tag `TraitMapping`.
required:
- medgens
- clinical_assertion_id
- trait_type
- mapping_type
- mapping_value
- mapping_ref
properties:
medgens:
type: array
items:
$ref: '#/components/schemas/ClinvarRcvTraitMappingMedgen'
description: nested elements
clinical_assertion_id:
type: integer
format: int64
description: ID of clinical assertion.
trait_type:
type: string
description: The trait type.
mapping_type:
$ref: '#/components/schemas/ClinvarRcvTraitMappingType'
description: The mapping type.
mapping_value:
type: string
description: The mapping value.
mapping_ref:
type: string
description: The mapping reference.
ClinvarRcvTraitMappingMedgen:
type: object
description: Local type for the tag "MedGen"
required:
- name
- cui
properties:
name:
type: string
description: Name.
cui:
type: string
description: CUI.
ClinvarRcvTraitMappingType:
type: string
description: Local type for the attribute `@MappingType`.
enum:
- name
- xref
ClinvarRecordHistory:
type: object
description: |-
A structure to support reporting of an accession, its version, the
date its status changed, and text describing that change.
Corresponds to `typeRecordHistory` in XSD.
nested elements
required:
- accession
- version
properties:
comment:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: Optional comment on the history record.
accession:
type: string
description: The accession.
version:
type: integer
format: int32
description: The version.
date_changed:
type:
- string
- 'null'
format: date-time
description: The date the record.
variation_id:
type:
- integer
- 'null'
format: int64
description: |-
Attribute @VaritionID is only populated for VCV, where @Accession
is like VCV000000009
ClinvarRelativeOrientation:
type: string
description: |-
Enumeration for relative orientation.
NB: unused in XML
enum:
- cis
- trans
- unknown
ClinvarResultType:
type: string
description: Local enumeration for result types.
enum:
- number_of_occurrences
- p_value
- odds_ratio
- variant_call
ClinvarSample:
type: object
description: |-
Description of a sample.
Corresponds to `typeSample` in XSD.
required:
- ages
- citations
- xrefs
- comments
properties:
sample_description:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSampleDescription'
description: The sample description.
origin:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarOrigin'
description: The sample origin.
ethnicity:
type:
- string
- 'null'
description: Sample ethnicity.
geographic_origin:
type:
- string
- 'null'
description: Sample geographic origin.
tissue:
type:
- string
- 'null'
description: Sample tissue.
somatic_variant_in_normal_tissue:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSomaticVariantInNormalTissue'
description: Presence of variant in normal tissue.
somatic_variant_allele_fraction:
type:
- string
- 'null'
description: Somatic variant allele fraction.
cell_line:
type:
- string
- 'null'
description: Cell line name.
species:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSpecies'
description: Species.
ages:
type: array
items:
$ref: '#/components/schemas/ClinvarAge'
description: Age (range), max. size of 2.
strain:
type:
- string
- 'null'
description: Strain.
affected_status:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAffectedStatus'
description: Affected status.
numer_tested:
type:
- integer
- 'null'
format: int32
description: Denominator, total individuals included in this observation set.
number_males:
type:
- integer
- 'null'
format: int32
description: Denominator, total males included in this observation set.
number_females:
type:
- integer
- 'null'
format: int32
description: Denominator, total females included in this observation set.
number_chr_tested:
type:
- integer
- 'null'
format: int32
description: |-
Denominator, total number chromosomes tested. Number affected
and unaffected are captured in the element NumberObserved.
gender:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarGender'
description: |-
Gender should be used ONLY if explicit values are not
available for number of males or females, and there is a need to indicate
that the genders in the sample are known.
family_data:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarFamilyData'
description: Family information.
proband:
type:
- string
- 'null'
description: Optional proband ID.
indication:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarIndication'
description: Optional indication.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
source_type:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSampleSourceType'
description: Source type.
ClinvarSampleDescription:
type: object
description: Local type for sample description.
properties:
description:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: Description of sample.
citation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarCitation'
description: Citation.
ClinvarSampleSourceType:
type: string
description: Local enumeration for SourceType.
enum:
- submitter_generated
- data_mining
ClinvarScv:
type: object
description: |-
Description of a SCV.
Corresponds to "typeSCV" in XSD.
required:
- accession
- version
properties:
title:
type:
- string
- 'null'
description: Optional title.
accession:
type: string
description: Accession.
version:
type: integer
format: int32
description: Version.
ClinvarSequenceLocation:
type: object
description: Local type for sequence location.
required:
- assembly
- chr
properties:
for_display:
type:
- boolean
- 'null'
description: forDisplay value.
assembly:
type: string
description: Name of assembly.
chr:
$ref: '#/components/schemas/ClinvarChromosome'
description: Chromosomeof variant.
accession:
type:
- string
- 'null'
description: Optional chromosome accession.
outer_start:
type:
- integer
- 'null'
format: int32
description: Outer start position.
minimum: 0
inner_start:
type:
- integer
- 'null'
format: int32
description: Inner start position.
minimum: 0
start:
type:
- integer
- 'null'
format: int32
description: Start position.
minimum: 0
stop:
type:
- integer
- 'null'
format: int32
description: Stop position.
minimum: 0
inner_stop:
type:
- integer
- 'null'
format: int32
description: Inner stop position.
minimum: 0
outer_stop:
type:
- integer
- 'null'
format: int32
description: Outer stop position.
minimum: 0
display_start:
type:
- integer
- 'null'
format: int32
description: Display start position.
minimum: 0
display_stop:
type:
- integer
- 'null'
format: int32
description: Display stop position.
minimum: 0
strand:
type:
- string
- 'null'
description: Strand.
variant_length:
type:
- integer
- 'null'
format: int32
description: Variant length.
minimum: 0
reference_allele:
type:
- string
- 'null'
description: Reference allele.
alternate_allele:
type:
- string
- 'null'
description: Alternate allele.
assembly_accession_version:
type:
- string
- 'null'
description: Assembly accession version.
assembly_status:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarAssemblyStatus'
description: Assembly status.
position_vcf:
type:
- integer
- 'null'
format: int32
description: Position in VCF.
minimum: 0
reference_allele_vcf:
type:
- string
- 'null'
description: Reference allele in VCF.
alternate_allele_vcf:
type:
- string
- 'null'
description: Alternate allele in VCF.
for_display_length:
type:
- integer
- 'null'
format: int32
description: For display length.
minimum: 0
ClinvarSeverity:
type: string
description: |-
Enumeration describing severity.
Corresponds to XSD type "typeSeverity"
enum:
- mild
- moderate
- severe
ClinvarSoftware:
type: object
description: Description of a software.
required:
- name
properties:
name:
type: string
description: Name of the software.
version:
type:
- string
- 'null'
description: Version of the software; optional.
purpose:
type:
- string
- 'null'
description: Purpose of the software; optional.
ClinvarSomaticVariantInNormalTissue:
type: string
description: Local enumeration for presence in normal tissue.
enum:
- present
- absent
- not_tested
ClinvarSpecies:
type: object
description: Definition of a species.
required:
- name
properties:
name:
type: string
description: Name of the species.
taxonomy_id:
type:
- integer
- 'null'
format: int32
description: Optional taxonomy ID.
ClinvarStatus:
type: string
description: |-
Enumeration describing status.
Corresponds to `typeStatus` in XSD.
enum:
- current
- completed_and_retired
- delete
- in_development
- reclassified
- reject
- secondary
- suppressed
- under_review
ClinvarSubmissionId:
type: object
description: Local type for ClinVarSubmissionID.
required:
- local_key
properties:
local_key:
type: string
description: |-
The identifier provided by the submitter to facilitate
identification of records corresponding to their submissions. If not
provided by a submitter, NCBI generates one. If provided by
submitter, that is represented in localKeyIsSubmitted.
title:
type:
- string
- 'null'
description: Optional title.
local_key_is_submitted:
type:
- boolean
- 'null'
description: Optional indication whether local key has been submitted.
submitted_assembly:
type:
- string
- 'null'
description: Optional assembly of submission.
ClinvarSubmitter:
type: object
description: |-
A structure to support reporting the name of a submitter, its
organization id, and its abbreviation and type.
required:
- type
properties:
submitter_identifiers:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSubmitterIdentifiers'
description: The submitter's identifier.
type:
$ref: '#/components/schemas/ClinvarSubmitterType'
description: The submitter type.
ClinvarSubmitterIdentifiers:
type: object
description: |-
Set of attributes for the primary submitter. Any addtional submitters
are captured in the AdditionalSubmitters element.
required:
- submitter_name
- org_id
- org_category
properties:
submitter_name:
type: string
description: Name of submitter.
org_id:
type: integer
format: int64
description: Organization ID.
org_category:
type: string
description: Organization category.
org_abbreviation:
type:
- string
- 'null'
description: Organization abbreviation; optional.
ClinvarSubmitterReviewStatus:
type: string
description: |-
Enumeration describing submitter review status.
Corresponds to `typeSubmitterReviewStatusValue` in XSD.
enum:
- no_classification_provided
- no_assertion_criteria_provided
- criteria_provided_single_submitter
- reviewed_by_expert_panel
- practice_guideline
- flagged_submission
- criteria_provided_multiple_submitters_no_conflicts
- criteria_provided_conflicting_classifications
- classified_by_single_submitter
- reviewed_by_professional_society
- not_classified_by_submitter
- classified_by_multiple_submitters
ClinvarSubmitterType:
type: string
description: Enumeration of submitter kind.
enum:
- primary
- secondary
- behalf
ClinvarTrait:
type: object
description: Type to describe traits in various places.
required:
- names
- symbols
- attributes
- trait_relationships
- citations
- xrefs
- comments
- sources
properties:
names:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: names
symbols:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: symbols
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: attributes
trait_relationships:
type: array
items:
$ref: '#/components/schemas/ClinvarTraitRelationship'
description: Trait relationships
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Citation list.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Xref list.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Comment list.
sources:
type: array
items:
type: string
description: Sources
ClinvarTraitRelationship:
type: object
description: Local type for trait relationship.
required:
- names
- citations
- xrefs
- comments
- sources
- type
properties:
names:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: Name(s) of the trait.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: Citation list.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: Xref list.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: Comment list.
sources:
type: array
items:
type: string
description: Sources
type:
$ref: '#/components/schemas/ClinvarTraitRelationshipType'
description: Trait type.
ClinvarTraitRelationshipType:
type: string
description: |-
Local enumeration for trait types.
NB: only DrugResponseAndDisease is used in the XML.
enum:
- phenotype
- subphenotype
- drug_response_and_disease
- co_occuring_condition
- finding_member
ClinvarTraitSet:
type: object
description: |-
A set of ``Trait`` objects.
NB: Called "ClinAsserTraitSetType" in the XSD.
required:
- traits
- names
- symbols
- attributes
- xrefs
- citations
- comments
- type
properties:
traits:
type: array
items:
$ref: '#/components/schemas/ClinvarTrait'
description: The traits.
names:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: The names.
symbols:
type: array
items:
$ref: '#/components/schemas/ClinvarGenericSetElement'
description: The symbols.
attributes:
type: array
items:
$ref: '#/components/schemas/ClinvarAttributeSetElement'
description: The attributes.
xrefs:
type: array
items:
$ref: '#/components/schemas/ClinvarXref'
description: List of xrefs.
citations:
type: array
items:
$ref: '#/components/schemas/ClinvarCitation'
description: List of citations.
comments:
type: array
items:
$ref: '#/components/schemas/ClinvarComment'
description: List of comments.
type:
$ref: '#/components/schemas/ClinvarTraitSetType'
description: The type.
date_last_evaluated:
type:
- string
- 'null'
format: date-time
description: Date of last evaluation.
id:
type:
- integer
- 'null'
format: int64
description: ID.
contributes_to_aggregate_classification:
type:
- boolean
- 'null'
description: Whether contributes to aggregate classification.
lower_level_of_evidence:
type:
- boolean
- 'null'
description: Lower level of evidence.
multiple_condition_explanation:
type:
- string
- 'null'
description: Explanation of or multiple conditions.
ClinvarTraitSetType:
type: string
description: Local type.
enum:
- disease
- drug_response
- finding
- phenotype_instruction
- trait_choice
ClinvarVariationArchive:
type: object
description: |-
This element groups the set of data specific to a VariationArchive
record, namely the summary data of what has been submitted about a
VariationID AND for Classified records only, the content each
submission (SCV) provided.
Type for the `<VariationArchive>` type.
required:
- variation_id
- variation_name
- variation_type
- accession
- version
- number_of_submitters
- number_of_submissions
- record_type
- record_status
- replaceds
properties:
variation_id:
type: integer
format: int64
description: Numeric variation ID.
variation_name:
type: string
description: |-
This is ClinVar's name for the variant. ClinVar uses this term in
its web displays
variation_type:
type: string
description: Type of the variant.
date_created:
type:
- string
- 'null'
format: date-time
description: |-
DateCreated is the date when the record first became public in
ClinVar.
date_last_updated:
type:
- string
- 'null'
format: date-time
description: |-
The date the record was last updated in the public database. The
update may be a change to one of the submitted records (SCVs) or
annotation added to the aggregate record by NCBI staff. This date
is independent of a version change; annotated added by NCBI may
change without representing a change in the version.
most_recent_submission:
type:
- string
- 'null'
format: date-time
description: |-
This date is of the most recent submitted record (SCV) for the
VCV; it may reflect a new submitted record or an update to a submitted record.
accession:
type: string
description: |-
Accession assigned to the variant, or set of variants, that was
Classified
version:
type: integer
format: int32
description: Version of record and suffix for accession.
number_of_submitters:
type: integer
format: int32
description: Number of submitters in record.
number_of_submissions:
type: integer
format: int32
description: Number of submissions in record.
record_type:
$ref: '#/components/schemas/ClinvarVariationArchiveRecordType'
description: Record type.
record_status:
$ref: '#/components/schemas/ClinvarVariationArchiveRecordStatus'
description: The record's status.
replaced_by:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarRecordHistory'
description: Pointer to the replacing record; optional.
replaceds:
type: array
items:
$ref: '#/components/schemas/ClinvarRecordHistory'
description: The list of VCV accessions this record has replaced.
comment:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarComment'
description: Comment on the record; optional.
species:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarSpecies'
description: Specification of the species.
classified_record:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarClassifiedRecord'
description: |-
This element describes the classification of a single
allele, haplotype, or genotype based on all submissions to ClinVar. This
differs from the element IncludedRecord, which describes simple alleles
or haplotypes, referenced in ClassifiedRecord, but for which no explicit
classification was submitted. Once that variation is described, details
are added about the phenotypes being classified, the classification, the
submitters providing the classifications, and all supported evidence.
NB: mutually exclusive with `included_record`.
included_record:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarIncludedRecord'
description: |-
This element describes a single allele or haplotype
included in submissions to ClinVar, but for which no explicit
classification was submitted. It also references the submissions and the
Classified records that include them.
NB: mutually exclusive with `classified_record`.
ClinvarVariationArchiveRecordStatus:
type: string
description: Enumeration for `@RecordStatus`.
enum:
- current
- previous
- replaced
- deleted
ClinvarVariationArchiveRecordType:
type: string
description: Enumeration for `@RecordType`.
enum:
- included
- classified
ClinvarVariationRelease:
type: object
description: |-
The element to group each VariationArchive element in the release
Type for the `<ClinVarVariationRelease>` tag.
attributes
required:
- variation_archives
properties:
release_date:
type:
- string
- 'null'
format: date-time
description: The current release.
variation_archives:
type: array
items:
$ref: '#/components/schemas/ClinvarVariationArchive'
description: List of `<VariationArchive>` tags.
ClinvarVariationType:
type: string
description: Enumeration describing variation type.
enum:
- diplotype
- compound_heterozygote
- distinct_chromosomes
ClinvarVersionedAccession:
type: object
description: Accession with version.
required:
- accession
- version
properties:
accession:
type: string
description: The accession.
version:
type: integer
format: int32
description: The version.
ClinvarXref:
type: object
description: |-
This structure is used to represent how an object described in the
submission relates to objects in other databases.
required:
- db
- id
properties:
db:
type: string
description: |-
The name of the database. When there is an overlap with sequence
databases, that name is used.
id:
type: string
description: |-
The identifier used by the database. Being exported as a string
even though internally the database has rules for defining which datases use
integer identifers.
type:
type:
- string
- 'null'
description: |-
Used to differentiate between different types of identifiers that
a database may provide.
url:
type:
- string
- 'null'
description: Optional URL to the database entry.
status:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarStatus'
description: The status; defaults to "current".
ClinvarZygosity:
type: string
description: Enumeration describing zygosity.
enum:
- homozygote
- single_heterozygote
- compound_heterozygote
- hemizygote
- not_provided
CustomError:
type: object
description: Custom error type for the Actix server.
required:
- err
properties:
err:
type: string
DbsnpRecord:
type: object
description: A record corresponding to dbSNP VCF.
required:
- chrom
- pos
- ref_allele
- alt_allele
- rs_id
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: Alternate allele.
rs_id:
type: integer
format: int32
description: The rs ID.
ExtractedVcvRecordList:
type: object
description: List of `ClinvarExtractedVcvRecord`s.
required:
- records
properties:
records:
type: array
items:
$ref: '#/components/schemas/ClinvarExtractedVcvRecord'
description: The list of VCV records that may share a global variant.
GeneNames:
type: object
description: Identifier / name information for one gene.
required:
- hgnc_id
- symbol
- name
- alias_symbol
- alias_name
properties:
hgnc_id:
type: string
description: HGNC gene ID.
symbol:
type: string
description: HGNC gene symbol.
name:
type: string
description: Gene name from HGNC.
alias_symbol:
type: array
items:
type: string
description: HGNC alias symbols.
alias_name:
type: array
items:
type: string
description: HGNC alias names.
ensembl_gene_id:
type:
- string
- 'null'
description: ENSEMBL gene ID.
ncbi_gene_id:
type:
- string
- 'null'
description: NCBI gene ID.
GenesAcmgSecondaryFindingRecord:
type: object
description: Information from ACMG secondary findings list.
required:
- hgnc_id
- ensembl_gene_id
- ncbi_gene_id
- gene_symbol
- mim_gene_id
- disease_phenotype
- disorder_mim
- phenotype_category
- inheritance
- sf_list_version
- variants_to_report
properties:
hgnc_id:
type: string
description: The HGNC ID.
ensembl_gene_id:
type: string
description: The Ensembl gene ID.
ncbi_gene_id:
type: string
description: The NCBI gene ID.
gene_symbol:
type: string
description: The HGNC gene symbol.
mim_gene_id:
type: string
description: The MIM gene ID.
disease_phenotype:
type: string
description: The disease phenotype.
disorder_mim:
type: string
description: The disease MIM id.
phenotype_category:
type: string
description: The phenotype category.
inheritance:
type: string
description: The mode of inheritance.
sf_list_version:
type: string
description: The version of the ACMG SF list of first appearance.
variants_to_report:
type: string
description: The variants to report according to ACMG SF.
GenesClingenDosageRecord:
type: object
description: '`ClinGen` gene dosage sensitivity record.'
required:
- gene_symbol
- ncbi_gene_id
- genomic_location_37
- genomic_location_38
properties:
gene_symbol:
type: string
description: Gene symbol.
ncbi_gene_id:
type: string
description: NCBI gene ID.
genomic_location_37:
type: string
description: Genomic location GRCh37.
genomic_location_38:
type: string
description: Genomic location GRCh38.
haploinsufficiency_score:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesClingenDosageScore'
description: Haploinsufficiency score.
triplosensitivity_score:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesClingenDosageScore'
description: Triplosensitivity score.
haploinsufficiency_disease_id:
type:
- string
- 'null'
description: Haploinsufficiency Disease ID.
triplosensitivity_disease_id:
type:
- string
- 'null'
description: Haploinsufficiency Disease ID.
GenesClingenDosageScore:
type: string
description: Enumeration for Haploinsufficiency / Triplosensitivity scores.
enum:
- SufficientEvidenceAvailable
- SomeEvidenceAvailable
- LittleEvidence
- NoEvidenceAvailable
- Recessive
- Unlikely
GenesClinvarPerGeneRecord:
type: object
description: ClinVar detailed information per gene.
required:
- per_release_vars
properties:
per_impact_counts:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGeneImpactCounts'
description: Counts of variants per impact
per_freq_counts:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesCoarseClinsigFrequencyCounts'
description: Counts of variants per impact / frequency
per_release_vars:
type: array
items:
$ref: '#/components/schemas/GenesExtractedVariantsPerRelease'
description: Variants for the given gene.
GenesClinvarQuery:
type: object
description: Parameters for `handle`.
properties:
hgnc_id:
type:
- array
- 'null'
items:
type: string
description: The HGNC IDs to search for.
GenesClinvarResponse:
type: object
description: Result for `handle_with_openapi`.
required:
- genes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/GenesClinvarResponseEntry'
description: The resulting per-gene ClinVar information.
GenesClinvarResponseEntry:
type: object
description: One entry in the result.
required:
- hgnc_id
- record
properties:
hgnc_id:
type: string
description: HGNC ID of the gene.
record:
$ref: '#/components/schemas/GenesClinvarPerGeneRecord'
description: The resulting per-gene record.
GenesCoarseClinsigFrequencyCounts:
type: object
required:
- hgnc_id
- pathogenic_counts
- uncertain_counts
- benign_counts
properties:
hgnc_id:
type: string
description: The gene HGNC ID.
pathogenic_counts:
type: array
items:
type: integer
format: int32
minimum: 0
description: The counts for (likely) pathogenic.
uncertain_counts:
type: array
items:
type: integer
format: int32
minimum: 0
description: The counts for uncertain significance.
benign_counts:
type: array
items:
type: integer
format: int32
minimum: 0
description: The counts for (likely) benign.
GenesConditionsRecord:
type: object
description: Record from the integrated conditions computation.
required:
- hgnc_id
- disease_associations
- panelapp_associations
properties:
hgnc_id:
type: string
description: The HGNC ID.
disease_associations:
type: array
items:
$ref: '#/components/schemas/GenesDiseaseAssociation'
description: The gene-disease associations.
panelapp_associations:
type: array
items:
$ref: '#/components/schemas/GenesPanelappAssociation'
description: The PanelApp associations.
GenesDbnsfpRecord:
type: object
description: Code for data from the dbNSFP database.
required:
- gene_name
- gene_old_names
- gene_other_names
- ccds_id
- refseq_id
- mim_id
- omim_id
- pathway_biocarta_short
- pathway_biocarta_full
- pathway_consensus_path_db
- pathway_kegg_id
- pathway_kegg_full
- function_description
- disease_description
- mim_phenotype_id
- mim_disease
- orphanet_disorder_id
- orphanet_disorder
- orphanet_association_type
- trait_association_gwas
- hpo_id
- hpo_name
- go_biological_process
- go_cellular_component
- go_molecular_function
- tissue_specificity_uniprot
- expression_egenetics
- expression_gnf_atlas
- interactions_intact
- interactions_biogrid
- interactions_consensus_path_db
properties:
gene_name:
type: string
description: Gene symbol from HGNC.
ensembl_gene:
type:
- string
- 'null'
description: Ensembl gene id (from HGNC).
chr:
type:
- string
- 'null'
description: Chromosome number (from HGNC).
gene_old_names:
type: array
items:
type: string
description: Old gene symbol (from HGNC).
gene_other_names:
type: array
items:
type: string
description: Other gene names (from HGNC).
uniprot_acc:
type:
- string
- 'null'
description: Uniprot acc (from HGNC).
uniprot_id:
type:
- string
- 'null'
description: Uniprot id (from HGNC).
entrez_gene_id:
type:
- string
- 'null'
description: Uniprot id (from HGNC).
ccds_id:
type: array
items:
type: string
description: CCDS id (from HGNC).
refseq_id:
type: array
items:
type: string
description: Refseq gene id (from HGNC).
ucsc_id:
type:
- string
- 'null'
description: UCSC gene id (from HGNC).
mim_id:
type: array
items:
type: string
description: MIM gene id (from OMIM).
omim_id:
type: array
items:
type: string
description: MIM gene id from OMIM.
gene_full_name:
type:
- string
- 'null'
description: Gene full name (from HGNC).
pathway_uniprot:
type:
- string
- 'null'
description: Pathway description from Uniprot.
pathway_biocarta_short:
type: array
items:
type: string
description: Short name of the Pathway(s) the gene belongs to (from BioCarta).
pathway_biocarta_full:
type: array
items:
type: string
description: Full name(s) of the Pathway(s) the gene belongs to (from BioCarta).
pathway_consensus_path_db:
type: array
items:
type: string
description: Pathway(s) the gene belongs to (from ConsensusPathDB).
pathway_kegg_id:
type: array
items:
type: string
description: ID(s) of the Pathway(s) the gene belongs to (from KEGG).
pathway_kegg_full:
type: array
items:
type: string
description: Full name(s) of the Pathway(s) the gene belongs to (from KEGG).
function_description:
type: array
items:
type: string
description: Function description of the gene (from Uniprot).
disease_description:
type: array
items:
type: string
description: Disease(s) the gene caused or associated with (from Uniprot).
mim_phenotype_id:
type: array
items:
type: string
description: MIM id(s) of the phenotype the gene caused or associated with (from Uniprot).
mim_disease:
type: array
items:
type: string
description: MIM disease name(s) with MIM id(s) in \[\] (from Uniprot).
orphanet_disorder_id:
type: array
items:
type: string
description: Orphanet Number of the disorder the gene caused or associated with.
orphanet_disorder:
type: array
items:
type: string
description: Disorder name from Orphanet.
orphanet_association_type:
type: array
items:
type: string
description: The type of association beteen the gene and the disorder in Orphanet.
trait_association_gwas:
type: array
items:
type: string
description: Trait(s) the gene associated with (from GWAS catalog).
hpo_id:
type: array
items:
type: string
description: ID of the mapped Human Phenotype Ontology.
hpo_name:
type: array
items:
type: string
description: Name of the mapped Human Phenotype Ontology.
go_biological_process:
type: array
items:
type: string
description: GO terms for biological process.
go_cellular_component:
type: array
items:
type: string
description: GO terms for cellular component.
go_molecular_function:
type: array
items:
type: string
description: GO terms for molecular function.
tissue_specificity_uniprot:
type: array
items:
type: string
description: Tissue specificity description from Uniprot.
expression_egenetics:
type: array
items:
type: string
description: Tissues/organs the gene expressed in (egenetics data from BioMart).
expression_gnf_atlas:
type: array
items:
type: string
description: Tissues/organs the gene expressed in (GNF/Atlas data from BioMart).
interactions_intact:
type: array
items:
type: string
description: The interacting genes from IntAct.
interactions_biogrid:
type: array
items:
type: string
description: The interacting genes from BioGRID.
interactions_consensus_path_db:
type: array
items:
type: string
description: The interacting genes from ConsensusPathDB.
haploinsufficiency:
type:
- number
- 'null'
format: double
description: |-
Estimated probability of haploinsufficiency of the gene (from
doi:10.1371/journal.pgen.1001154).
hipred_score:
type:
- number
- 'null'
format: double
description: |-
Estimated probability of haploinsufficiency of the gene (from
doi:10.1093/bioinformatics/btx028).
hipred:
type:
- string
- 'null'
description: |-
HIPred prediction of haploinsufficiency of the gene. Y(es) or N(o). (from
doi:10.1093/bioinformatics/btx028).
ghis:
type:
- number
- 'null'
format: double
description: |-
A score predicting the gene haploinsufficiency. The higher the score the more likely the
gene is haploinsufficient (from doi: 10.1093/nar/gkv474).
prec:
type:
- number
- 'null'
format: double
description: |-
Estimated probability that gene is a recessive disease gene (from
DOI:10.1126/science.1215040).
known_rec_info:
type:
- string
- 'null'
description: |-
Known recessive status of the gene (from DOI:10.1126/science.1215040) "lof-tolerant =
seen in homozygous state in at least one 1000G individual" "recessive = known OMIM
recessive disease" (original annotations from DOI:10.1126/science.1215040).
rvis_evs:
type:
- number
- 'null'
format: double
description: |-
Residual Variation Intolerance Score, a measure of intolerance of mutational burden, the
higher the score the more tolerant to mutational burden the gene is. Based on EVS
(ESP6500) data. from doi:10.1371/journal.pgen.1003709.
rvis_percentile_evs:
type:
- number
- 'null'
format: double
description: |-
The percentile rank of the gene based on RVIS, the higher the percentile the more
tolerant to mutational burden the gene is. Based on EVS (ESP6500) data.
lof_fdr_exac:
type:
- number
- 'null'
format: double
description: |-
"A gene's corresponding FDR p-value for preferential LoF depletion among the ExAC
population. Lower FDR corresponds with genes that are increasingly depleted of LoF
variants." cited from RVIS document.
rvis_exac:
type:
- number
- 'null'
format: double
description: |-
"ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six
individual ethnic strata from ExAC." cited from RVIS document.
rvis_percentile_exac:
type:
- number
- 'null'
format: double
description: |-
"Genome-Wide percentile for the new ExAC-based RVIS; setting 'common' MAF filter at 0.05%
in at least one of the six individual ethnic strata from ExAC." cited from RVIS document.
exac_pli:
type:
- number
- 'null'
format: double
description: |-
"the probability of being loss-of-function intolerant (intolerant of both heterozygous
and homozygous lof variants)" based on ExAC r0.3 data.
exac_prec:
type:
- number
- 'null'
format: double
description: |-
"the probability of being intolerant of homozygous, but not heterozygous lof variants"
based on ExAC r0.3 data.
exac_pnull:
type:
- number
- 'null'
format: double
description: |-
"the probability of being tolerant of both heterozygous and homozygous lof variants"
based on ExAC r0.3 data.
exac_nontcga_pli:
type:
- number
- 'null'
format: double
description: |-
"the probability of being loss-of-function intolerant (intolerant of both heterozygous
and homozygous lof variants)" based on ExAC r0.3 nonTCGA subset.
exac_nontcga_prec:
type:
- number
- 'null'
format: double
description: |-
"the probability of being intolerant of homozygous, but not heterozygous lof variants"
based on ExAC r0.3 nonTCGA subset.
exac_nontcga_pnull:
type:
- number
- 'null'
format: double
description: |-
"the probability of being tolerant of both heterozygous and homozygous lof variants"
based on ExAC r0.3 nonTCGA subset.
exac_nonpsych_pli:
type:
- number
- 'null'
format: double
description: |-
"the probability of being loss-of-function intolerant (intolerant of both heterozygous
and homozygous lof variants)" based on ExAC r0.3 nonpsych subset.
exac_nonpsych_prec:
type:
- number
- 'null'
format: double
description: |-
"the probability of being intolerant of homozygous, but not heterozygous lof variants"
based on ExAC r0.3 nonpsych subset.
exac_nonpsych_pnull:
type:
- number
- 'null'
format: double
description: |-
"the probability of being tolerant of both heterozygous and homozygous lof variants"
based on ExAC r0.3 nonpsych subset/
gnomad_pli:
type:
- number
- 'null'
format: double
description: |-
"the probability of being loss-of-function intolerant (intolerant of both heterozygous
and homozygous lof variants)" based on gnomAD 2.1 data.
gnomad_prec:
type:
- number
- 'null'
format: double
description: |-
"the probability of being intolerant of homozygous, but not heterozygous lof variants"
based on gnomAD 2.1 data.
gnomad_pnull:
type:
- number
- 'null'
format: double
description: |-
"the probability of being tolerant of both heterozygous and homozygous lof variants"
based on gnomAD 2.1 data.
exac_del_score:
type:
- number
- 'null'
format: double
description: '"Winsorised deletion intolerance z-score" based on ExAC r0.3.1 CNV data.'
exac_dup_score:
type:
- number
- 'null'
format: double
description: '"Winsorised duplication intolerance z-score" based on ExAC r0.3.1 CNV data.'
exac_cnv_score:
type:
- number
- 'null'
format: double
description: '"Winsorised cnv intolerance z-score" based on ExAC r0.3.1 CNV data.'
exac_cnv_flag:
type:
- string
- 'null'
description: |-
"Gene is in a known region of recurrent CNVs mediated by tandem segmental duplications
and intolerance scores are more likely to be biased or noisy." from ExAC r0.3.1 CNV
release.
gdi:
type:
- number
- 'null'
format: double
description: |-
gene damage index score, "a genome-wide, gene-level metric of the mutational damage that
has accumulated in the general population" from doi: 10.1073/pnas.1518646112. The higher
the score the less likely the gene is to be responsible for monogenic diseases.
gdi_phred:
type:
- number
- 'null'
format: double
description: Phred-scaled GDI scores.
gdp_all_disease_causing:
type:
- string
- 'null'
description: gene damage prediction (low/medium/high) by GDI for all diseases.,
gdp_all_mendelian:
type:
- string
- 'null'
description: gene damage prediction (low/medium/high) by GDI for all Mendelian diseases.
gdp_all_mendelian_ad:
type:
- string
- 'null'
description: |-
gene damage prediction (low/medium/high) by GDI for Mendelian autosomal dominant
diseases.
gdp_mendelian_ar:
type:
- string
- 'null'
description: |-
gene damage prediction (low/medium/high) by GDI for Mendelian autosomal recessive
diseases.
gdp_pid:
type:
- string
- 'null'
description: |-
gene damage prediction (low/medium/high) by GDI for all primary immunodeficiency
diseases.
gdp_pid_ad:
type:
- string
- 'null'
description: |-
gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal
dominant diseases.
gdp_pid_ar:
type:
- string
- 'null'
description: |-
gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal
recessive diseases.
gdp_cancer:
type:
- string
- 'null'
description: gene damage prediction (low/medium/high) by GDI for all cancer disease.
gdb_cancer_rec:
type:
- string
- 'null'
description: gene damage prediction (low/medium/high) by GDI for cancer recessive disease.
gdp_cancer_dom:
type:
- string
- 'null'
description: gene damage prediction (low/medium/high) by GDI for cancer dominant disease.
loftool_score:
type:
- number
- 'null'
format: double
description: |-
A percentile score for gene intolerance to functional change. The lower the score the
higher gene intolerance to functional change. For details see doi:
10.1093/bioinformatics/btv602.
sorva_lof_maf_5_het_or_hom:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method
for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_maf_5_hom_or_comphet:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a
method for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_maf_1_het_or_hom:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method
for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_maf_1_hom_or_comphet:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a
method for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_or_mis_maf_5_het_or_hom:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from
a method for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_or_mis_maf_5_hom_or_comphet:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This
fraction is from a method for ranking genes based on mutational burden called SORVA
(Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_or_mis_maf_1_het_or_hom:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from
a method for ranking genes based on mutational burden called SORVA (Significance Of Rare
VAriants). Please see doi: 10.1101/103218 for details.
sorva_lof_or_mis_maf_1_hom_or_comphet:
type:
- number
- 'null'
format: double
description: |-
The fraction of individuals in the 1000 Genomes Project data (N=2504) who are either
Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This
fraction is from a method for ranking genes based on mutational burden called SORVA
(Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details.
essential_gene:
type:
- string
- 'null'
description: |-
Essential ("E") or Non-essential phenotype-changing ("N") based on Mouse Genome
Informatics database. from doi:10.1371/journal.pgen.1003484.
essential_gene_crispr:
type:
- string
- 'null'
description: |-
Essential ("E") or Non-essential phenotype-changing ("N") based on large scale CRISPR
experiments. from doi: 10.1126/science.aac7041.
essential_gene_crispr2:
type:
- string
- 'null'
description: |-
Essential ("E"), context-Specific essential ("S"), or Non-essential phenotype-changing
("N") based on large scale CRISPR experiments. from
<http://dx.doi.org/10.1016/j.cell.2015.11.015.>
essential_gene_gene_trap:
type:
- string
- 'null'
description: |-
Essential ("E"), HAP1-Specific essential ("H"), KBM7-Specific essential ("K"), or
Non-essential phenotype-changing ("N"), based on large scale mutagenesis experiments.
from doi: 10.1126/science.aac7557.
gene_indispensability_score:
type:
- number
- 'null'
format: double
description: |-
A probability prediction of the gene being essential. From
doi:10.1371/journal.pcbi.1002886.
gene_indispensability_pred:
type:
- string
- 'null'
description: Essential ("E") or loss-of-function tolerant ("N") based on Gene_indispensability_score.
mgi_mouse_gene:
type:
- string
- 'null'
description: Homolog mouse gene name from MGI.
mgi_mouse_phenotype:
type:
- string
- 'null'
description: Phenotype description for the homolog mouse gene from MGI.
zfin_zebrafish_gene:
type:
- string
- 'null'
description: Homolog zebrafish gene name from ZFIN.
zfin_zebrafish_structure:
type:
- string
- 'null'
description: Affected structure of the homolog zebrafish gene from ZFIN.
zfin_zebrafish_phenotype_quality:
type:
- string
- 'null'
description: Phenotype description for the homolog zebrafish gene from ZFIN.
zfin_zebrafish_phenotype_tag:
type:
- string
- 'null'
description: Phenotype tag for the homolog zebrafish gene from ZFIN"
GenesDecipherHiRecord:
type: object
description: Decipher HI Predictions
required:
- hgnc_id
- hgnc_symbol
- p_hi
- hi_index
properties:
hgnc_id:
type: string
description: HGNC identifier.
hgnc_symbol:
type: string
description: Official HGNC gene symbol.
p_hi:
type: number
format: double
description: P(HI) prediction from DECIPHER HI.
hi_index:
type: number
format: double
description: Percent HI index.
GenesDiseaseAssociation:
type: object
description: A gene-disease association.
required:
- hgnc_id
- labeled_disorders
- sources
- confidence
properties:
hgnc_id:
type: string
description: The HGNC ID.
labeled_disorders:
type: array
items:
$ref: '#/components/schemas/GenesLabeledDisorder'
description: The gene-disease association entries.
disease_name:
type:
- string
- 'null'
description: Overall disease name.
disease_definition:
type:
- string
- 'null'
description: Disease definition.
sources:
type: array
items:
$ref: '#/components/schemas/GenesDiseaseAssociationSource'
description: The gene-disease association sources.
confidence:
$ref: '#/components/schemas/GenesDiseaseAssociationConfidenceLevel'
description: Overall disease-gene association confidence level.
GenesDiseaseAssociationConfidenceLevel:
type: string
description: Enumeration for confidence levels.
enum:
- High
- Medium
- Low
GenesDiseaseAssociationEntryConfidenceLevel:
type: string
description: Enumeration for confidence levels.
enum:
- High
- Medium
- Low
GenesDiseaseAssociationSource:
type: string
description: Enumeration for sources.
enum:
- Omim
- Orphanet
- Panelapp
GenesDominoRecord:
type: object
description: Information from DOMINO.
required:
- gene_symbol
- score
properties:
gene_symbol:
type: string
description: Gene symbol.
score:
type: number
format: double
description: The score.
GenesEntityType:
type: string
description: Enumeration for entity types.
enum:
- Gene
- Str
- Region
GenesExtractedVariantsPerRelease:
type: object
description: Extracted variants per release.
required:
- variants
properties:
release:
type:
- string
- 'null'
description: Release version.
variants:
type: array
items:
$ref: '#/components/schemas/ClinvarExtractedVcvRecord'
description: Variants per gene.
GenesFields:
type: string
description: The allowed fields to search in.
enum:
- hgnc_id
- symbol
- name
- alias_symbol
- alias_name
- ensembl_gene_id
- ncbi_gene_id
GenesGeneData:
type: object
description: Gene identity information.
properties:
hgnc_id:
type:
- string
- 'null'
description: HGNC ID.
hgnc_symbol:
type:
- string
- 'null'
description: HGNC gene symbol.
gene_symbol:
type:
- string
- 'null'
description: Gene symbol.
GenesGeneDiseaseAssociationEntry:
type: object
description: A gene-disease association entry.
required:
- source
- confidence
properties:
source:
$ref: '#/components/schemas/GenesDiseaseAssociationSource'
description: The gene-disease association source.
confidence:
$ref: '#/components/schemas/GenesDiseaseAssociationEntryConfidenceLevel'
description: The gene-disease association confidence level.
GenesGeneImpact:
type: string
description: Enumeration with the variant consequence.
enum:
- Unspecified
- ThreePrimeUtrVariant
- FivePrimeUtrVariant
- DownstreamTranscriptVariant
- FrameshiftVariant
- InframeIndel
- StartLost
- IntronVariant
- MissenseVariant
- NonCodingTranscriptVariant
- StopGained
- NoSequenceAlteration
- SpliceAcceptorVariant
- SpliceDonorVariant
- StopLost
- SynonymousVariant
- UpstreamTranscriptVariant
GenesGeneImpactCounts:
type: object
description: Entry for storing counts of `GeneImpact` and `ClinicalSignificance`.
required:
- hgnc_id
- impact_counts
properties:
hgnc_id:
type: string
description: The gene HGNC ID.
impact_counts:
type: array
items:
$ref: '#/components/schemas/GenesImpactCounts'
description: The impact counts.
GenesGeneInfoRecord:
type: object
description: Information about a gene.
required:
- panelapp
properties:
acmg_sf:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord'
description: Information from the ACMG secondary finding list.
clingen:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesClingenDosageRecord'
description: Information from ClinGen dosage curation.
dbnsfp:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDbnsfpRecord'
description: Information from dbNSFP.
gnomad_constraints:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGnomadConstraintsRecord'
description: Information from the gnomAD constraints database.
hgnc:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesHgncRecord'
description: Information from the HGNC database.
ncbi:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesNcbiRecord'
description: Information from the NCBI gene database (aka "Entrez").
omim:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesOmimRecord'
description: Information about gene to OMIM term annotation, composed from clingen and HPO.
orpha:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesOrphaRecord'
description: Information about gene to Orphanet annotation, derived from Orphapacket.
rcnv:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesRcnvRecord'
description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022).
shet:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesShetRecord'
description: Information from the sHet score (Weghor et al., 2019)
gtex:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGtexRecord'
description: Information from GTEx data
domino:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDominoRecord'
description: Information from DOMINO.
decipher_hi:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDecipherHiRecord'
description: DECIPHER HI score.
panelapp:
type: array
items:
$ref: '#/components/schemas/GenesPanelAppRecord'
description: GenomicsEngland PanelApp gene information.
conditions:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesConditionsRecord'
description: Conditions record.
GenesGeneRecord:
type: object
description: Entry in the genes RocksDB database.
required:
- panelapp
properties:
acmg_sf:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesAcmgSecondaryFindingRecord'
description: Information from the ACMG secondary finding list.
clingen:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesClingenDosageRecord'
description: Information from ClinGen dosage curation.
dbnsfp:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDbnsfpRecord'
description: Information from dbNSFP.
gnomad_constraints:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGnomadConstraintsRecord'
description: Information from the gnomAD constraints database.
hgnc:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesHgncRecord'
description: Information from the HGNC database.
ncbi:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesNcbiRecord'
description: Information from the NCBI gene database (aka "Entrez").
omim:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesOmimRecord'
description: Information about gene to OMIM term annotation, composed from clingen and HPO.
orpha:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesOrphaRecord'
description: Information about gene to Orphanet annotation, derived from Orphapacket.
rcnv:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesRcnvRecord'
description: Information from the rCNV dosage sensitivity scores (Collins et al., 2022).
shet:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesShetRecord'
description: Information from the sHet score (Weghor et al., 2019)
gtex:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGtexRecord'
description: Information from GTEx data
domino:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDominoRecord'
description: Information from DOMINO.
decipher_hi:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesDecipherHiRecord'
description: DECIPHER HI score.
panelapp:
type: array
items:
$ref: '#/components/schemas/GenesPanelAppRecord'
description: GenomicsEngland PanelApp gene information.
conditions:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesConditionsRecord'
description: Conditions record.
GenesGnomadConstraintsRecord:
type: object
description: Code for data from the gnomAD constraints.
required:
- ensembl_gene_id
- entrez_id
- gene_symbol
properties:
ensembl_gene_id:
type: string
description: The Ensembl gene ID.
entrez_id:
type: string
description: The NCBI gene ID.
gene_symbol:
type: string
description: The HGNC gene symbol.
exp_lof:
type:
- number
- 'null'
format: double
description: The expected number of loss-of-function variants.
exp_mis:
type:
- number
- 'null'
format: double
description: The expected number of missense variants.
exp_syn:
type:
- number
- 'null'
format: double
description: The expected number of synonymous variants.
mis_z:
type:
- number
- 'null'
format: double
description: The missense-related Z-score.
obs_lof:
type:
- integer
- 'null'
format: int32
description: The observed number of loss-of-function variants.
minimum: 0
obs_mis:
type:
- integer
- 'null'
format: int32
description: The observed number of missense variants.
minimum: 0
obs_syn:
type:
- integer
- 'null'
format: int32
description: The observed number of synonymous variants.
minimum: 0
oe_lof:
type:
- number
- 'null'
format: double
description: The loss-of-function observed/expected ratio.
oe_lof_lower:
type:
- number
- 'null'
format: double
description: The lower bound of the loss-of-function observed/expected ratio.
oe_lof_upper:
type:
- number
- 'null'
format: double
description: The upper bound of the loss-of-function observed/expected ratio.
oe_mis:
type:
- number
- 'null'
format: double
description: The missense observed/expected ratio.
oe_mis_lower:
type:
- number
- 'null'
format: double
description: The lower bound of the missense observed/expected ratio.
oe_mis_upper:
type:
- number
- 'null'
format: double
description: The upper bound of the missense observed/expected ratio.
oe_syn:
type:
- number
- 'null'
format: double
description: The synonymous observed/expected ratio.
oe_syn_lower:
type:
- number
- 'null'
format: double
description: The lower bound of the synonymous observed/expected ratio.
oe_syn_upper:
type:
- number
- 'null'
format: double
description: The upper bound of the synonymous observed/expected ratio.
pli:
type:
- number
- 'null'
format: double
description: The probability of loss-of-function intolerance (pLI score).
syn_z:
type:
- number
- 'null'
format: double
description: The synonymous-related Z-score.
exac_pli:
type:
- number
- 'null'
format: double
description: The probability of loss-of-function intolerance (pLI score) from ExAC.
exac_obs_lof:
type:
- number
- 'null'
format: double
description: The observed number of loss-of-function variants from ExAC.
exac_exp_lof:
type:
- number
- 'null'
format: double
description: The expected number of loss-of-function variants from ExAC.
exac_oe_lof:
type:
- number
- 'null'
format: double
description: The loss-of-function observed/expected ratio from ExAC.
GenesGtexRecord:
type: object
description: Entry with the GTEx information.
required:
- hgnc_id
- ensembl_gene_id
- ensembl_gene_version
- records
properties:
hgnc_id:
type: string
description: The HGNC ID.
ensembl_gene_id:
type: string
description: ENSEMBL gene ID.
ensembl_gene_version:
type: string
description: ENSEMBL gene version.
records:
type: array
items:
$ref: '#/components/schemas/GenesGtexTissueRecord'
description: Counts per tissue
GenesGtexTissue:
type: string
description: Enumeration for GTEx V8 tissue
enum:
- AdiposeTissue
- AdrenalGland
- Bladder
- Blood
- BloodVessel
- BoneMarrow
- Brain
- Breast
- CervixUteri
- Colon
- Esophagus
- FallopianTube
- Heart
- Kidney
- Liver
- Lung
- Muscle
- Nerve
- Ovary
- Pancreas
- Pituitary
- Prostate
- SalivaryGland
- Skin
- SmallIntestine
- Spleen
- Stomach
- Testis
- Thyroid
- Uterus
- Vagina
GenesGtexTissueDetailed:
type: string
description: Enumeration for GTEx V8 tissue details
enum:
- AdiposeSubcutaneous
- AdiposeVisceralOmentum
- AdrenalGland
- ArteryAorta
- ArteryCoronary
- ArteryTibial
- Bladder
- BrainAmygdala
- BrainAnteriorCingulateCortex
- BrainCaudateBasalGanglia
- BrainCerebellarHemisphere
- BrainCerebellum
- BrainCortex
- BrainFrontalCortex
- BrainHippocampus
- BrainHypothalamus
- BrainNucleusAccumbens
- BrainPutamenBasalGanglia
- BrainSpinalCord
- BrainSubstantiaNigra
- BreastMammaryTissue
- CellsCulturedFibroblasts
- CellsEbvTransformedLymphocytes
- CellsLeukemiaCellLine
- CervixEctocervix
- CervixEndocervix
- ColonSigmoid
- ColonTransverse
- EsophagusGastroesophagealJunction
- EsophagusMucosa
- EsophagusMuscularis
- FallopianTube
- HeartAtrialAppendage
- HeartLeftVentricle
- KidneyCortex
- KidneyMedulla
- Liver
- Lung
- MinorSalivaryGland
- MuscleSkeletal
- NerveTibial
- Ovary
- Pancreas
- Pituitary
- Prostate
- SalivaryGland
- SkinNotSunExposedSuprapubic
- SkinSunExposedLowerLeg
- SmallIntestineTerminalIleum
- Spleen
- Stomach
- Testis
- Thyroid
- Uterus
- Vagina
- WholeBlood
GenesGtexTissueRecord:
type: object
description: Entry with the tissue-specific information for a gene.
required:
- tissue
- tissue_detailed
- tpms
properties:
tissue:
$ref: '#/components/schemas/GenesGtexTissue'
description: The tissue type
tissue_detailed:
$ref: '#/components/schemas/GenesGtexTissueDetailed'
description: The detailed tissue type
tpms:
type: array
items:
type: number
format: float
description: TPM counts
GenesHgncLsdb:
type: object
description: Information from the locus-specific dabase.
required:
- name
- url
properties:
name:
type: string
description: The name of the Locus Specific Mutation Database.
url:
type: string
description: The URL for the gene.
GenesHgncRecord:
type: object
description: A record from the HGNC database.
required:
- hgnc_id
- symbol
- name
- status
- alias_symbol
- alias_name
- prev_symbol
- prev_name
- gene_group
- gene_group_id
- ena
- refseq_accession
- ccds_id
- uniprot_ids
- pubmed_id
- mgd_id
- rgd_id
- lsdb
- omim_id
- enzyme_id
- mane_select
properties:
hgnc_id:
type: string
description: HGNC ID. A unique ID created by the HGNC for every approved symbol.
symbol:
type: string
description: The HGNC approved gene symbol.
name:
type: string
description: HGNC approved name for the gene.
locus_group:
type:
- string
- 'null'
description: |-
A group name for a set of related locus types as defined by the HGNC
(e.g. non-coding RNA).
locus_type:
type:
- string
- 'null'
description: The locus type as defined by the HGNC (e.g. RNA, transfer).
status:
type: integer
format: int32
description: Status of the symbol report.
location:
type:
- string
- 'null'
description: Cytogenetic location of the gene (e.g. 2q34).
location_sortable:
type:
- string
- 'null'
description: Sortable cytogenic location of the gene (e.g. 02q34).
alias_symbol:
type: array
items:
type: string
description: Other symbols used to refer to this gene.
alias_name:
type: array
items:
type: string
description: Other names used to refer to this gene.
prev_symbol:
type: array
items:
type: string
description: Prevous symbols used to refer to this gene.
prev_name:
type: array
items:
type: string
description: Previous names used to refer to this gene.
gene_group:
type: array
items:
type: string
description: Name given to a gene group.
gene_group_id:
type: array
items:
type: integer
format: int32
minimum: 0
description: ID used to designate a gene group.
date_approved_reserved:
type:
- string
- 'null'
description: The date the entry was first approved.
date_symbol_changed:
type:
- string
- 'null'
description: The date the gene symbol was last changed.
date_name_changed:
type:
- string
- 'null'
description: The date the gene name was last changed.
date_modified:
type:
- string
- 'null'
description: Date the entry was last modified.
entrez_id:
type:
- string
- 'null'
description: Entrez gene id.
ensembl_gene_id:
type:
- string
- 'null'
description: Ensembl gene id.
vega_id:
type:
- string
- 'null'
description: Vega gene id.
ucsc_id:
type:
- string
- 'null'
description: UCSC gene id.
ena:
type: array
items:
type: string
description: ENA accession number(s).
refseq_accession:
type: array
items:
type: string
description: RefSeq nucleotide accession(s).
ccds_id:
type: array
items:
type: string
description: Consensus CDS ID(ds).
uniprot_ids:
type: array
items:
type: string
description: Uniprot IDs.
pubmed_id:
type: array
items:
type: integer
format: int32
minimum: 0
description: Pubmed IDs.
mgd_id:
type: array
items:
type: string
description: Mouse genome informatics database ID(s).
rgd_id:
type: array
items:
type: string
description: Rat genome database gene ID(s).
lsdb:
type: array
items:
$ref: '#/components/schemas/GenesHgncLsdb'
description: The name of the Locus Specific Mutation Database and URL for the gene.
cosmic:
type:
- string
- 'null'
description: Symbol used within COSMIC.
omim_id:
type: array
items:
type: string
description: OMIM ID(s).
mirbase:
type:
- string
- 'null'
description: miRBase ID.
homeodb:
type:
- integer
- 'null'
format: int32
description: Homeobox Database ID.
minimum: 0
snornabase:
type:
- string
- 'null'
description: snoRNABase ID.
bioparadigms_slc:
type:
- string
- 'null'
description: |-
Symbol used to link to the SLC tables database at bioparadigms.org
for the gene.
orphanet:
type:
- integer
- 'null'
format: int32
description: Orphanet ID.
minimum: 0
pseudogene_org:
type:
- string
- 'null'
description: Pseudogene.org.
horde_id:
type:
- string
- 'null'
description: Symbol used within HORDE for the gene.
merops:
type:
- string
- 'null'
description: ID used to link to the MEROPS peptidase database.
imgt:
type:
- string
- 'null'
description: Symbol used within international ImMunoGeneTics information system.
iuphar:
type:
- string
- 'null'
description: |-
The objectId used to link to the IUPHAR/BPS Guide to PHARMACOLOGY
database.
cd:
type:
- string
- 'null'
description: Symbol used within the Human Cell Differentiation Molecule database.
mamit_trnadb:
type:
- integer
- 'null'
format: int32
description: ID to link to the Mamit-tRNA database
minimum: 0
lncrnadb:
type:
- string
- 'null'
description: lncRNA Database ID.
enzyme_id:
type: array
items:
type: string
description: ENZYME EC accession number.
intermediate_filament_db:
type:
- string
- 'null'
description: ID used to link to the Human Intermediate Filament Database.
agr:
type:
- string
- 'null'
description: The HGNC ID that the Alliance of Genome Resources (AGR) use.
mane_select:
type: array
items:
type: string
description: |-
NCBI and Ensembl transcript IDs/acessions including the version
number.
GenesHgncStatus:
type: string
description: Status of the symbol report, which can be either "Approved" or "Entry Withdrawn".
enum:
- Approved
- Withdrawn
GenesImpactCounts:
type: object
description: Stores the counts for a gene impact.
required:
- gene_impact
- count_benign
- count_likely_benign
- count_uncertain_significance
- count_likely_pathogenic
- count_pathogenic
properties:
gene_impact:
$ref: '#/components/schemas/GenesGeneImpact'
description: The gene impact.
count_benign:
type: integer
format: int32
description: The counts for the benign impact.
minimum: 0
count_likely_benign:
type: integer
format: int32
description: The counts for the likely benign impact.
minimum: 0
count_uncertain_significance:
type: integer
format: int32
description: The counts for the uncertain significance impact.
minimum: 0
count_likely_pathogenic:
type: integer
format: int32
description: The counts for the likely pathogenic impact.
minimum: 0
count_pathogenic:
type: integer
format: int32
description: The counts for the pathogenic impact.
minimum: 0
GenesInfoResponse:
type: object
description: Query response for `handle_with_openapi()`.
required:
- genes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/GenesGeneInfoRecord'
description: Version information of the genes.
GenesLabeledDisorder:
type: object
description: A labeled disorder.
required:
- term_id
properties:
term_id:
type: string
description: The disorder ID.
title:
type:
- string
- 'null'
description: The disorder name.
GenesLookupResponse:
type: object
description: Result for `async fn handle_with_openapi(
required:
- genes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/GenesLookupResultEntry'
description: The resulting gene information.
GenesLookupResultEntry:
type: object
description: One result entry in the response.
required:
- query
properties:
query:
type: string
description: The query string,
gene_names:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GeneNames'
description: The gene names information.
GenesNcbiRecord:
type: object
description: A record from the NCBI gene database.
required:
- gene_id
- rif_entries
properties:
gene_id:
type: string
description: NCBI Gene ID.
summary:
type:
- string
- 'null'
description: Gene summary.
rif_entries:
type: array
items:
$ref: '#/components/schemas/GenesRifEntry'
description: '"Reference Into Function" entry.'
GenesOmimRecord:
type: object
description: A record from the OMIM gene association.
required:
- hgnc_id
- omim_diseases
properties:
hgnc_id:
type: string
description: The HGNC gene ID.
omim_diseases:
type: array
items:
$ref: '#/components/schemas/GenesOmimTerm'
description: The associated OMIM records.
GenesOmimTerm:
type: object
description: Description of an OMIM record.
required:
- omim_id
- label
properties:
omim_id:
type: string
description: The OMIM ID.
label:
type: string
description: The OMIM label.
GenesOrphaRecord:
type: object
description: A record from the ORDO gene association.
required:
- hgnc_id
- orpha_diseases
properties:
hgnc_id:
type: string
description: The HGNC gene ID.
orpha_diseases:
type: array
items:
$ref: '#/components/schemas/GenesOrphaTerm'
description: The associated ORPHA diseases.
GenesOrphaTerm:
type: object
description: Description of an ORDO record.
required:
- orpha_id
- label
properties:
orpha_id:
type: string
description: The ORPHA ID.
label:
type: string
description: The disease name.
GenesPanel:
type: object
description: Message for panel information.
required:
- id
- name
- disease_group
- disease_sub_group
- version
- version_created
- relevant_disorders
- types
properties:
id:
type: integer
format: int32
description: Panel ID.
minimum: 0
hash_id:
type:
- string
- 'null'
description: Panel hash ID.
name:
type: string
description: Panel name.
disease_group:
type: string
description: Disease group.
disease_sub_group:
type: string
description: Disease subgroup.
version:
type: string
description: Version
version_created:
type: string
description: Creation date of version.
relevant_disorders:
type: array
items:
type: string
description: Relevant disorders.
stats:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesPanelStats'
description: Stats.
types:
type: array
items:
$ref: '#/components/schemas/GenesPanelType'
description: Panel types.
GenesPanelAppRecord:
type: object
description: Entry in PanelApp.
required:
- entity_type
- entity_name
- confidence_level
- publications
- evidence
- phenotypes
- mode_of_inheritance
properties:
gene_data:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesGeneData'
description: Gene identity information.
entity_type:
$ref: '#/components/schemas/GenesEntityType'
description: Entity type.
entity_name:
type: string
description: Entity name.
confidence_level:
$ref: '#/components/schemas/GenesPanelappRecordConfidenceLevel'
description: Confidence level.
penetrance:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesPenetrance'
description: Penetrance.
publications:
type: array
items:
type: string
description: Publications.
evidence:
type: array
items:
type: string
description: Evidence.
phenotypes:
type: array
items:
type: string
description: Phenotypes.
mode_of_inheritance:
type: string
description: Mode of inheritance.
panel:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesPanel'
description: Panel.
GenesPanelStats:
type: object
description: Message for panel statistics.
required:
- number_of_genes
- number_of_strs
- number_of_regions
properties:
number_of_genes:
type: integer
format: int32
description: Number of genes.
minimum: 0
number_of_strs:
type: integer
format: int32
description: Number of STRs.
minimum: 0
number_of_regions:
type: integer
format: int32
description: Number of regions.
minimum: 0
GenesPanelType:
type: object
description: Message for panel types.
required:
- name
- slug
- description
properties:
name:
type: string
description: Type name.
slug:
type: string
description: Slug.
description:
type: string
description: Description.
GenesPanelappAssociation:
type: object
description: An association of a gene by HGNC with a panel from PanelApp.
required:
- hgnc_id
- confidence_level
- entity_type
- phenotypes
properties:
hgnc_id:
type: string
description: The HGNC ID.
confidence_level:
$ref: '#/components/schemas/GenesPanelappAssociationConfidenceLevel'
description: The PanelApp confidence level.
entity_type:
$ref: '#/components/schemas/GenesPanelappEntityType'
description: The PanelApp entity type.
mode_of_inheritance:
type:
- string
- 'null'
description: The PanelApp entity name.
phenotypes:
type: array
items:
type: string
description: The PanelApp publications.
panel:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GenesPanelappPanel'
description: The PanelApp panel.
GenesPanelappAssociationConfidenceLevel:
type: string
description: Enumeration for PanelApp confidence level.
enum:
- Green
- Amber
- Red
- None
GenesPanelappEntityType:
type: string
description: Enumeration for entity type.
enum:
- Gene
- Region
- Str
GenesPanelappPanel:
type: object
description: A panel from PanelApp.
required:
- id
- name
- version
properties:
id:
type: integer
format: int32
description: PanelApp panel ID.
name:
type: string
description: PanelApp panel name.
version:
type: string
description: PanelApp panel version.
GenesPanelappRecordConfidenceLevel:
type: string
description: Enumeration for PanelApp confidence level.
enum:
- Green
- Amber
- Red
- None
GenesPenetrance:
type: string
description: Enumeration for penetrance.
enum:
- Complete
- Incomplete
GenesRcnvRecord:
type: object
description: Entry in the rCNV dosage sensitivity scores (Collins et al., 2022).
required:
- hgnc_id
- p_haplo
- p_triplo
properties:
hgnc_id:
type: string
description: The HGNC ID.
p_haplo:
type: number
format: double
description: The pHaplo value.
p_triplo:
type: number
format: double
description: The pTriplo value.
GenesRifEntry:
type: object
description: Reference into function record.
required:
- text
- pmids
properties:
text:
type: string
description: The RIF text.
pmids:
type: array
items:
type: integer
format: int32
minimum: 0
description: PubMed IDs.
GenesSearchQuery:
type: object
description: Parameters for `handle`.
required:
- q
properties:
q:
type: string
description: The string to search for.
fields:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/GenesFields'
description: The fields to search in.
case_sensitive:
type:
- boolean
- 'null'
description: Enable case sensitive search.
GenesSearchResponse:
type: object
description: Result for `handle`.
required:
- genes
properties:
genes:
type: array
items:
$ref: '#/components/schemas/Scored'
description: The resulting gene information.
GenesShetRecord:
type: object
description: Entry with sHet information (Weghorn et al., 2019).
required:
- hgnc_id
- s_het
properties:
hgnc_id:
type: string
description: The HGNC ID.
s_het:
type: number
format: double
description: The sHet value.
GenomeRelease:
type: string
description: Local genome release for command line arguments.
enum:
- grch37
- grch38
Gnomad2AgeInfo:
type: object
description: Encapsulate VCF INFO fields related to age.
required:
- age_hist_hom_bin_freq
- age_hist_het_bin_freq
properties:
age_hist_hom_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0].
age_hist_hom_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_hom_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_het_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]
age_hist_het_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
heteroplasmic variant.
age_hist_het_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
heteroplasmic variant.
Gnomad2AlleleCounts:
type: object
description: Store the relevant allele counts and frequencies in a given sub cohort.
required:
- ac
- an
- nhomalt
- af
properties:
ac:
type: integer
format: int32
description: Number of alternate alleles in sub cohort.
an:
type: integer
format: int32
description: Total number of alleles in the sub cohort.
nhomalt:
type: integer
format: int32
description: Number of homozygous alternate alleles in the sub cohort.
af:
type: number
format: float
description: Alternate allele frequency in the sub cohort.
Gnomad2AlleleCountsBySex:
type: object
description: Store the allele counts for the given sub cohort and sub cohort factored by sex.
properties:
overall:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCounts'
description: Overall allele counts in the sub cohort.
xx:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCounts'
description: Allele counts in female/XX karyotype individuals of sub cohort.
xy:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCounts'
description: Allele counts in male/XY karyotype individuals of sub cohort.
Gnomad2CohortAlleleCounts:
type: object
description: Store the allele counts for the given cohort.
required:
- by_population
properties:
cohort:
type:
- string
- 'null'
description: Name of the cohort.
by_population:
type: array
items:
$ref: '#/components/schemas/Gnomad2PopulationAlleleCounts'
description: Allele counts for each population.
by_sex:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCountsBySex'
description: Allele counts by sex.
raw:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCounts'
description: Raw allele counts.
popmax:
type:
- string
- 'null'
description: The population with maximum AF.
af_popmax:
type:
- number
- 'null'
format: float
description: |-
Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and
indeterminate ancestry).
ac_popmax:
type:
- integer
- 'null'
format: int32
description: Allele count in population with maximum AF.
an_popmax:
type:
- integer
- 'null'
format: int32
description: Total number of alleles in population with maximum AF.
nhomalt_popmax:
type:
- integer
- 'null'
format: int32
description: Total number of homozygous individuals in population with maximum AF.
Gnomad2DepthInfo:
type: object
description: Encapsulate VCF INFO fields related to depth.
required:
- dp_hist_all_bin_freq
- dp_hist_alt_bin_freq
properties:
dp_hist_all_n_larger:
type:
- integer
- 'null'
format: int32
description: Count of dp values falling above highest histogram bin edge for all individuals.
dp_hist_alt_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of dp values falling above highest histogram bin edge for individuals with the
alternative allele
dp_hist_all_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0,
1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
dp_hist_alt_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0,
200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
Gnomad2Filter:
type: string
description: Protocol buffer enum for site-level filters.
enum:
- allele_count_is_zero
- inbreeding_coeff
- pass
- random_forest
Gnomad2LiftoverInfo:
type: object
description: Liftover related information.
required:
- reverse_complemented_alleles
- swapped_alleles
- original_alleles
properties:
reverse_complemented_alleles:
type: boolean
description: |-
The REF and the ALT alleles have been reverse complemented in liftover since the mapping from
the previous reference to the current one was on the negative strand.
swapped_alleles:
type: boolean
description: |-
The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It
is possible that not all INFO annotations reflect this swap, and in the genotypes, only the
GT, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that
was used during the LiftOver to be sure.
original_alleles:
type: array
items:
type: string
description: |-
A list of the original alleles (including REF) of the variant prior to liftover. If the
alleles were not changed during liftover, this attribute will be omitted.
original_contig:
type:
- string
- 'null'
description: The name of the source contig/chromosome prior to liftover.
original_start:
type:
- string
- 'null'
description: The position of the variant on the source contig prior to liftover.
Gnomad2PopulationAlleleCounts:
type: object
description: Store the allele counts for the given population.
required:
- population
properties:
population:
type: string
description: Name of the population.
counts:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AlleleCountsBySex'
description: The overall allele counts and the one by sex.
faf95:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 95% CI).
faf99:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 99% CI).
Gnomad2QualityInfo:
type: object
description: Encapsulate quality-related information.
required:
- vqsr_positive_train_site
- vqsr_negative_train_site
- segdup
- lcr
- decoy
- transmitted_singleton
properties:
fs:
type:
- number
- 'null'
format: float
description: Phred-scaled p-value of Fisher's exact test for strand bias.
inbreeding_coeff:
type:
- number
- 'null'
format: float
description: |-
Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared
against the Hardy-Weinberg expectation.
mq:
type:
- number
- 'null'
format: float
description: Root mean square of the mapping quality of reads across all samples.
mq_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference read mapping qualities.
qd:
type:
- number
- 'null'
format: float
description: Variant call confidence normalized by depth of sample reads supporting a variant.
read_pos_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference read position bias.
vqsr_positive_train_site:
type: boolean
description: Variant was used to build the positive training set of high-quality variants for VQSR.
vqsr_negative_train_site:
type: boolean
description: Variant was used to build the negative training set of low-quality variants for VQSR.
base_q_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference base qualities.
clipping_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference number of hard clipped bases.
sor:
type:
- number
- 'null'
format: float
description: Strand bias estimated by the symmetric odds ratio test
dp:
type:
- integer
- 'null'
format: int32
description: |-
Depth of informative coverage for each sample; reads with MQ=255 or with bad mates are
filtered.
vqslod:
type:
- number
- 'null'
format: float
description: |-
Log-odds ratio of being a true variant versus being a false positive under the trained VQSR
Gaussian mixture model.
vqsr_culprit:
type:
- string
- 'null'
description: Allele-specific worst-performing annotation in the VQSR Gaussian mixture model
segdup:
type: boolean
description: Variant falls within a segmental duplication region
lcr:
type: boolean
description: Variant falls within a low complexity region.
decoy:
type: boolean
description: Variant falls within a reference decoy region.
transmitted_singleton:
type: boolean
description: |-
Variant was a callset-wide doubleton that was transmitted within a family (i.e., a singleton
amongst unrelated sampes in cohort).
pab_max:
type:
- number
- 'null'
format: float
description: |-
Maximum p-value over callset for binomial test of observed allele balance for a heterozygous
genotype, given expectation of AB=0.5.
Gnomad2RandomForestInfo:
type: object
description: Random forest related information.
required:
- rf_tp_probability
- rf_positive_label
- rf_negative_label
- rf_train
properties:
rf_tp_probability:
type: number
format: float
description: Random forest prediction probability for a site being a true variant.
rf_positive_label:
type: boolean
description: Variant was labelled as a positive example for training of random forest model.
rf_negative_label:
type: boolean
description: Variant was labelled as a negative example for training of random forest model.
rf_label:
type:
- string
- 'null'
description: Random forest training label.
rf_train:
type: boolean
description: Variant was used in training random forest model.
Gnomad2Record:
type: object
description: |-
Protocol buffer for the gnomAD v2 VCF record.
The more specialized fields from the INFO column are stored in separate, optional fields such
that we don't end up with a humongous message.
required:
- chrom
- pos
- ref_allele
- alt_allele
- filters
- vep
- allele_counts
- nonpar
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: Alternate allele.
filters:
type: array
items:
$ref: '#/components/schemas/Gnomad2Filter'
description: Site-level filters.
vep:
type: array
items:
$ref: '#/components/schemas/Gnomad2Vep'
description: VEP annotation records.
allele_counts:
type: array
items:
$ref: '#/components/schemas/Gnomad2CohortAlleleCounts'
description: |-
Variant allele counts in the different cohorts and population.
The populations in gnomAD v2/3 are: empty for global, "controls", "non_cancer", "non_neuro",
and "non_topmed".
nonpar:
type: boolean
description: Variant (on sex chromosome) falls outside a pseudoautosomal region
liftover_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2LiftoverInfo'
description: Information on lift-over from GRCh37 to GRCh38.
rf_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2RandomForestInfo'
description: Random forest related information.
variant_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2VariantInfo'
description: Variant-related information details.
quality_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2QualityInfo'
description: Summary information for variant quality interpretation.
age_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2AgeInfo'
description: Age-related information.
depth_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad2DepthInfo'
description: Depth of coverage-related information.
Gnomad2VariantInfo:
type: object
description: Variant type related information.
required:
- variant_type
- allele_type
- n_alt_alleles
- was_mixed
- has_star
properties:
variant_type:
type: string
description: Variant type (snv, indel, multi-snv, multi-indel, or mixed).
allele_type:
type: string
description: Allele type (snv, ins, del, or mixed).
n_alt_alleles:
type: integer
format: int32
description: Total number of alternate alleles observed at variant locus.
was_mixed:
type: boolean
description: Variant type was mixed.
has_star:
type: boolean
description: |-
Variant locus coincides with a spanning deletion (represented by a star) observed elsewhere
in the callset.
Gnomad2Vep:
type: object
description: Protocol buffer for the gnomAD-mtDNA VEP predictions.
required:
- allele
- consequence
- impact
- symbol
- gene
- feature_type
- feature
- feature_biotype
- canonical
- domains
properties:
allele:
type: string
description: Allele of record.
consequence:
type: string
description: Consequence, e.g., `"missense_variant"`.
impact:
type: string
description: Impact, e.g., `"MODERATE"`.
symbol:
type: string
description: Gene symbol, e.g., `"PCSK9"`.
gene:
type: string
description: Gene ID, `e.g., "ENSG00000169174"`.
feature_type:
type: string
description: Feature type, e.g., `"Transcript"`.
feature:
type: string
description: Feature ID, e.g., `"ENST00000302118"`.
feature_biotype:
type: string
description: Feature biotype, e.g., `"protein_coding"`.
exon:
type:
- string
- 'null'
description: Ranked exon number, e.g., `"1/4"`.
intron:
type:
- string
- 'null'
description: Ranked intron number, e.g., `"1/4"`.
hgvsc:
type:
- string
- 'null'
description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`.
hgvsp:
type:
- string
- 'null'
description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`.
cdna_position:
type:
- string
- 'null'
description: cDNA position, e.g., `"89/1863"`.
cds_position:
type:
- string
- 'null'
description: CDS position, e.g., `"89/1863"`.
protein_position:
type:
- string
- 'null'
description: Protein position, e.g., `"30/620"`.
amino_acids:
type:
- string
- 'null'
description: Amino acids, e.g., `"T/R"`.
codons:
type:
- string
- 'null'
description: Codons, e.g., `"gCg/gGg"`.
existing_variation:
type:
- string
- 'null'
description: Existing variation info.
dbsnp_id:
type:
- string
- 'null'
description: dbSNP ID, e.g., `"rs28942080"`.
distance:
type:
- string
- 'null'
description: Distance output of VEP.
strand:
type:
- string
- 'null'
description: Strand, e.g., `"1"`.
flags:
type:
- string
- 'null'
description: Flags, e.g., `"cds_end_NF"`.
variant_class:
type:
- string
- 'null'
description: Variant class, e.g., `"SNV"`.
minimised:
type:
- string
- 'null'
description: Minimised output of VEP.
symbol_source:
type:
- string
- 'null'
description: Symbol source, e.g., `"HGNC"`.
hgnc_id:
type:
- string
- 'null'
description: HGNC ID, e.g., `"HGNC:8706"`.
canonical:
type: boolean
description: Whether this is the canonical transcript.
tsl:
type:
- integer
- 'null'
format: int32
description: Transcript support level, e.g., `"1"`.
appris:
type:
- string
- 'null'
description: APPRIS annotation, e.g. `"P1"`.
ccds:
type:
- string
- 'null'
description: CCDS ID, e.g., `"CCDS30547.1"`.
ensp:
type:
- string
- 'null'
description: Ensembl protein ID, e.g., `"ENSP00000302118"`.
swissprot:
type:
- string
- 'null'
description: SwissProt ID, e.g., `"P04114"`.
trembl:
type:
- string
- 'null'
description: TREMBL ID, e.g., `"Q5T4W7"`.
uniparc:
type:
- string
- 'null'
description: UniParc ID, e.g., `"UPI000002D4B2"`.
gene_pheno:
type:
- string
- 'null'
description: Gene phenotype from VEP.
sift:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VepCommonPrediction'
description: SIFT prediction, e.g., `"tolerated(0.06)"`.
polyphen:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VepCommonPrediction'
description: PolyPhen prediction, e.g., `"benign(0.001)"`.
domains:
type: array
items:
$ref: '#/components/schemas/VepCommonDomain'
description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`.
hgvs_offset:
type:
- string
- 'null'
description: HGVS offset.
gmaf:
type:
- number
- 'null'
format: float
description: Overall minor allele frequency.
afr_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in AFR population.
amr_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in AMR population.
eas_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in EAS population.
eur_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in EUR population.
sas_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in SAS population.
aa_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in AA population.
ea_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in EA population.
exac_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC.
exac_adj_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency EXAC ADJ population.
exac_afr_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC AFR population.
exac_amr_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC AMR population.
exac_eas_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC EAS population.
exac_fin_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC FIN population.
exac_nfe_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC NFE population.
exac_oth_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC OTH population.
exac_sas_maf:
type:
- number
- 'null'
format: float
description: Minor allele frequency in ExAC SAS population.
clin_sig:
type:
- string
- 'null'
description: Clinical significance.
somatic:
type:
- string
- 'null'
description: Whether the variant is somatic.
pheno:
type:
- string
- 'null'
description: Phenotype.
pubmed:
type:
- string
- 'null'
description: Pubmed ID.
motif_name:
type:
- string
- 'null'
description: Motif name.
motif_pos:
type:
- string
- 'null'
description: Motif pos.
high_inf_pos:
type:
- string
- 'null'
description: '"high inf pos" from VEP.'
motif_score_change:
type:
- string
- 'null'
description: Motif score change.
lof:
type:
- string
- 'null'
description: Loss of function prediction.
lof_filter:
type:
- string
- 'null'
description: Loss of function filter.
lof_flags:
type:
- string
- 'null'
description: Loss of function flags.
lof_info:
type:
- string
- 'null'
description: Loss of function info.
Gnomad3AgeInfo:
type: object
description: Encapsulate VCF INFO fields related to age.
required:
- age_hist_hom_bin_freq
- age_hist_het_bin_freq
properties:
age_hist_hom_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0].
age_hist_hom_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_hom_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_het_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]
age_hist_het_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
heteroplasmic variant.
age_hist_het_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
heteroplasmic variant.
Gnomad3AlleleCounts:
type: object
description: Store the relevant allele counts and frequencies in a given sub cohort.
required:
- ac
- an
- nhomalt
- af
properties:
ac:
type: integer
format: int32
description: Number of alternate alleles in sub cohort.
an:
type: integer
format: int32
description: Total number of alleles in the sub cohort.
nhomalt:
type: integer
format: int32
description: Number of homozygous alternate alleles in the sub cohort.
af:
type: number
format: float
description: Alternate allele frequency in the sub cohort.
Gnomad3AlleleCountsBySex:
type: object
description: Store the allele counts for the given sub cohort and sub cohort factored by sex.
properties:
overall:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCounts'
description: Overall allele counts in the sub cohort.
xx:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCounts'
description: Allele counts in female/XX karyotype individuals of sub cohort.
xy:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCounts'
description: Allele counts in male/XY karyotype individuals of sub cohort.
Gnomad3CohortAlleleCounts:
type: object
description: Store the allele counts for the given cohort.
required:
- by_population
properties:
cohort:
type:
- string
- 'null'
description: Name of the cohort.
by_population:
type: array
items:
$ref: '#/components/schemas/Gnomad3PopulationAlleleCounts'
description: Allele counts for each population.
by_sex:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCountsBySex'
description: Allele counts by sex.
raw:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCounts'
description: Raw allele counts.
popmax:
type:
- string
- 'null'
description: The population with maximum AF.
af_popmax:
type:
- number
- 'null'
format: float
description: |-
Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and
indeterminate ancestry).
ac_popmax:
type:
- integer
- 'null'
format: int32
description: Allele count in population with maximum AF.
an_popmax:
type:
- integer
- 'null'
format: int32
description: Total number of alleles in population with maximum AF.
nhomalt_popmax:
type:
- integer
- 'null'
format: int32
description: Total number of homozygous individuals in population with maximum AF.
Gnomad3DepthInfo:
type: object
description: Encapsulate VCF INFO fields related to depth.
required:
- dp_hist_all_bin_freq
- dp_hist_alt_bin_freq
properties:
dp_hist_all_n_larger:
type:
- integer
- 'null'
format: int32
description: Count of dp values falling above highest histogram bin edge for all individuals.
dp_hist_alt_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of dp values falling above highest histogram bin edge for individuals with the
alternative allele
dp_hist_all_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0,
1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
dp_hist_alt_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0,
200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
Gnomad3EffectInfo:
type: object
description: Store details on variant effect predictions.
properties:
primate_ai_score:
type:
- number
- 'null'
format: float
description: PrimateAI's deleteriousness score from 0 (less deleterious) to 1 (more deleterious).
revel_score:
type:
- number
- 'null'
format: float
description: |-
dbNSFP's Revel score from 0 to 1. Variants with higher scores are predicted to be
more likely to be deleterious.
splice_ai_max_ds:
type:
- number
- 'null'
format: float
description: |-
Illumina's SpliceAI max delta score; interpreted as the probability of the variant
being splice-altering.
splice_ai_consequence:
type:
- string
- 'null'
description: The consequence term associated with the max delta score in 'splice_ai_max_ds'.
cadd_raw:
type:
- number
- 'null'
format: float
description: Raw CADD scores are interpretable as the extent to which the annotation profile for a given variant suggests that the variant is likely to be 'observed' (negative values) vs 'simulated' (positive values). Larger values are more deleterious.
cadd_phred:
type:
- number
- 'null'
format: float
description: Cadd Phred-like scores ('scaled C-scores') ranging from 1 to 99, based on the rank of each variant relative to all possible 8.6 billion substitutions in the human reference genome. Larger values are more deleterious.
Gnomad3Filter:
type: string
description: Protocol buffer enum for site-level filters.
enum:
- allele_count_is_zero
- as_vsqr
- inbreeding_coeff
- pass
Gnomad3PopulationAlleleCounts:
type: object
description: Store the allele counts for the given sub cohort in the given population.
required:
- population
properties:
population:
type: string
description: Name of the population.
counts:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCountsBySex'
description: The overall allele counts and the one by sex.
faf95:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 95% CI).
faf99:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 99% CI).
faf95_xx:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XX samples (using Poisson 95% CI).
faf99_xx:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XX samples (using Poisson 99% CI).
faf95_xy:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XY samples (using Poisson 95% CI).
faf99_xy:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XY samples (using Poisson 99% CI).
Gnomad3QualityInfo:
type: object
description: Encapsulate quality-related information.
required:
- positive_train_site
- negative_train_site
- segdup
- lcr
- transmitted_singleton
properties:
as_fs:
type:
- number
- 'null'
format: float
description: Allele-specific phred-scaled p-value of Fisher's exact test for strand bias.
inbreeding_coeff:
type:
- number
- 'null'
format: float
description: |-
Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared
against the Hardy-Weinberg expectation.
as_mq:
type:
- number
- 'null'
format: float
description: Allele-specific root mean square of the mapping quality of reads across all samples
mq_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference read mapping qualities.
as_mq_rank_sum:
type:
- number
- 'null'
format: float
description: |-
Allele-specific z-score from Wilcoxon rank sum test of alternate vs. reference read
mapping qualities.
as_qd:
type:
- number
- 'null'
format: float
description: |-
Allele-specific variant call confidence normalized by depth of sample reads supporting a
variant.
read_pos_rank_sum:
type:
- number
- 'null'
format: float
description: Z-score from Wilcoxon rank sum test of alternate vs. reference read position bias.
as_read_pos_rank_sum:
type:
- number
- 'null'
format: float
description: Allele-specific z-score from Wilcoxon rank sum test of alternate vs. reference read position bias.
as_sor:
type:
- number
- 'null'
format: float
description: Allele-specific strand bias estimated by the symmetric odds ratio test.
positive_train_site:
type: boolean
description: Variant was used to build the positive training set of high-quality variants for VQSR.
negative_train_site:
type: boolean
description: Variant was used to build the negative training set of low-quality variants for VQSR.
as_vqslod:
type:
- number
- 'null'
format: float
description: Allele-specific log-odds ratio of being a true variant versus being a false positive under the trained VQSR Gaussian mixture model.
as_culprit:
type:
- string
- 'null'
description: Allele-specific worst-performing annotation in the VQSR Gaussian mixture model.
segdup:
type: boolean
description: Variant falls within a segmental duplication region.
lcr:
type: boolean
description: Variant falls within a low complexity region.
transmitted_singleton:
type: boolean
description: |-
Variant was a callset-wide doubleton that was transmitted within a family (i.e., a singleton
amongst unrelated sampes in cohort).
as_pab_max:
type:
- number
- 'null'
format: float
description: Maximum p-value over callset for binomial test of observed allele balance for a heterozygous genotype, given expectation of 0.5.
as_qual_approx:
type:
- integer
- 'null'
format: int32
description: Allele-specific sum of PL\[0\] values; used to approximate the QUAL score.
as_sb_table:
type:
- string
- 'null'
description: Allele-specific forward/reverse read counts for strand bias tests.
sor:
type:
- number
- 'null'
format: float
description: Strand bias estimated by the symmetric odds ratio test (v4 only).
Gnomad3Record:
type: object
description: |-
Protocol buffer for the gnomAD-nuclear VCF record.
The more specialized fields from the INFO column are stored in separate, optional fields such
that we don't end up with a humongous message.
required:
- chrom
- pos
- ref_allele
- alt_allele
- filters
- vep
- allele_counts
- nonpar
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: Alternate allele.
filters:
type: array
items:
$ref: '#/components/schemas/Gnomad3Filter'
description: Site-level filters.
vep:
type: array
items:
$ref: '#/components/schemas/Gnomad3Vep'
description: VEP annotation records.
allele_counts:
type: array
items:
$ref: '#/components/schemas/Gnomad3CohortAlleleCounts'
description: |-
Variant allele counts in the different cohorts and population.
The populations in gnomAD v2/3 are: empty for global, "controls", "non_cancer", "non_neuro",
and "non_topmed".
nonpar:
type: boolean
description: Variant (on sex chromosome) falls outside a pseudoautosomal region
effect_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3EffectInfo'
description: Information on variant scores.
variant_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3VariantInfo'
description: Variant-related information details.
quality_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3QualityInfo'
description: Summary information for variant quality interpretation.
age_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AgeInfo'
description: Age-related information.
depth_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3DepthInfo'
description: Depth of coverage-related information.
Gnomad3VariantInfo:
type: object
description: Variant type related information.
required:
- variant_type
- allele_type
- n_alt_alleles
- was_mixed
- monoallelic
- var_dp
properties:
variant_type:
type: string
description: Variant type (snv, indel, multi-snv, multi-indel, or mixed).
allele_type:
type: string
description: Allele type (snv, ins, del, or mixed).
n_alt_alleles:
type: integer
format: int32
description: Total number of alternate alleles observed at variant locus.
was_mixed:
type: boolean
description: Variant type was mixed.
monoallelic:
type: boolean
description: All samples are homozygous alternate for the variant.
var_dp:
type: integer
format: int32
description: Depth over variant genotypes (does not include depth of reference samples).
as_vardp:
type:
- integer
- 'null'
format: int32
description: Allele-specific depth over variant genotypes (does not include depth of reference samples) (v4 only).
Gnomad3Vep:
type: object
description: Protocol buffer for the gnomAD-nuclear VEP predictions.
required:
- allele
- consequence
- impact
- symbol
- gene
- feature_type
- feature
- feature_biotype
- domains
properties:
allele:
type: string
description: Allele of record.
consequence:
type: string
description: Consequence, e.g., `"missense_variant"`.
impact:
type: string
description: Impact, e.g., `"MODERATE"`.
symbol:
type: string
description: Gene symbol, e.g., `"PCSK9"`.
gene:
type: string
description: Gene ID, `e.g., "ENSG00000169174"`.
feature_type:
type: string
description: Feature type, e.g., `"Transcript"`.
feature:
type: string
description: Feature ID, e.g., `"ENST00000302118"`.
feature_biotype:
type: string
description: Feature biotype, e.g., `"protein_coding"`.
exon:
type:
- string
- 'null'
description: Ranked exon number, e.g., `"1/4"`.
intron:
type:
- string
- 'null'
description: Ranked intron number, e.g., `"1/4"`.
hgvsc:
type:
- string
- 'null'
description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`.
hgvsp:
type:
- string
- 'null'
description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`.
cdna_position:
type:
- string
- 'null'
description: cDNA position, e.g., `"89/1863"`.
cds_position:
type:
- string
- 'null'
description: CDS position, e.g., `"89/1863"`.
protein_position:
type:
- string
- 'null'
description: Protein position, e.g., `"30/620"`.
amino_acids:
type:
- string
- 'null'
description: Amino acids, e.g., `"T/R"`.
codons:
type:
- string
- 'null'
description: Codons, e.g., `"gCg/gGg"`.
dbsnp_id:
type:
- string
- 'null'
description: |-
TODO: actually is optional int32 allele_num = 18;
dbSNP ID, e.g., `"rs28942080"`.
distance:
type:
- string
- 'null'
description: Distance output of VEP.
strand:
type:
- string
- 'null'
description: Strand, e.g., `"1"`.
variant_class:
type:
- string
- 'null'
description: Variant class, e.g., `"SNV"`.
minimised:
type:
- string
- 'null'
description: Minimised output of VEP.
symbol_source:
type:
- string
- 'null'
description: Symbol source, e.g., `"HGNC"`.
hgnc_id:
type:
- string
- 'null'
description: HGNC ID, e.g., `"HGNC:8706"`.
canonical:
type:
- boolean
- 'null'
description: Whether this is the canonical transcript.
tsl:
type:
- integer
- 'null'
format: int32
description: Transcript support level, e.g., `"1"`.
appris:
type:
- string
- 'null'
description: APPRIS annotation, e.g. `"P1"`.
ccds:
type:
- string
- 'null'
description: CCDS ID, e.g., `"CCDS30547.1"`.
ensp:
type:
- string
- 'null'
description: Ensembl protein ID, e.g., `"ENSP00000302118"`.
swissprot:
type:
- string
- 'null'
description: SwissProt ID, e.g., `"P04114"`.
trembl:
type:
- string
- 'null'
description: TREMBL ID, e.g., `"Q5T4W7"`.
uniparc:
type:
- string
- 'null'
description: UniParc ID, e.g., `"UPI000002D4B2"`.
gene_pheno:
type:
- string
- 'null'
description: Gene phenotype from VEP.
sift:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VepCommonPrediction'
description: SIFT prediction, e.g., `"tolerated(0.06)"`.
polyphen:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VepCommonPrediction'
description: PolyPhen prediction, e.g., `"benign(0.001)"`.
domains:
type: array
items:
$ref: '#/components/schemas/VepCommonDomain'
description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`.
hgvs_offset:
type:
- string
- 'null'
description: HGVS offset.
motif_name:
type:
- string
- 'null'
description: Motif name.
motif_pos:
type:
- string
- 'null'
description: Motif name.
high_inf_pos:
type:
- string
- 'null'
description: '"high inf pos" from VEP.'
motif_score_change:
type:
- string
- 'null'
description: Motif score change.
lof:
type:
- string
- 'null'
description: Loss of function prediction.
lof_filter:
type:
- string
- 'null'
description: Loss of function filter.
lof_flags:
type:
- string
- 'null'
description: Loss of function flags.
lof_info:
type:
- string
- 'null'
description: Loss of function info.
Gnomad4AncestryGroupAlleleCounts:
type: object
description: Store the allele counts for the given sub cohort in the given ancestry group.
required:
- ancestry_group
properties:
ancestry_group:
type: string
description: Name of the ancestry group.
counts:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCountsBySex'
description: The overall allele counts and the one by sex.
faf95:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 95% CI).
faf99:
type:
- number
- 'null'
format: float
description: The filtering allele frequency (using Poisson 99% CI).
faf95_xx:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XX samples (using Poisson 95% CI).
faf99_xx:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XX samples (using Poisson 99% CI).
faf95_xy:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XY samples (using Poisson 95% CI).
faf99_xy:
type:
- number
- 'null'
format: float
description: The filtering allele frequency for XY samples (using Poisson 99% CI).
Gnomad4CohortAlleleCounts:
type: object
description: Store the allele counts for the given cohort.
required:
- by_ancestry_group
properties:
cohort:
type:
- string
- 'null'
description: Name of the cohort.
by_ancestry_group:
type: array
items:
$ref: '#/components/schemas/Gnomad4AncestryGroupAlleleCounts'
description: Allele counts for each population.
by_sex:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCountsBySex'
description: Allele counts by sex.
raw:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AlleleCounts'
description: Raw allele counts.
grpmax:
type:
- string
- 'null'
description: The ancestry group with maximum AF.
af_grpmax:
type:
- number
- 'null'
format: float
description: Maximum allele frequency across ancestry groups.
ac_grpmax:
type:
- integer
- 'null'
format: int32
description: Allele count in ancestry group with maximum AF.
an_grpmax:
type:
- integer
- 'null'
format: int32
description: Total number of alleles in ancestry group with maximum AF.
nhomalt_grpmax:
type:
- integer
- 'null'
format: int32
description: Total number of homozygous individuals in ancestry group with maximum AF.
Gnomad4EffectInfo:
type: object
description: Store details on variant effect predictions.
properties:
pangolin_largest_ds:
type:
- number
- 'null'
format: float
description: Pangolin's largest delta score across 2 splicing consequences, which reflects the probability of the variant being splice-altering">
phylop:
type:
- number
- 'null'
format: float
description: Base-wise conservation score across the 241 placental mammals in the Zoonomia project. Score ranges from -20 to 9.28, and reflects acceleration (faster evolution than expected under neutral drift, assigned negative scores) as well as conservation (slower than expected evolution, assigned positive scores).">
polyphen_max:
type:
- number
- 'null'
format: float
description: Score that predicts the possible impact of an amino acid substitution on the structure and function of a human protein, ranging from 0.0 (tolerated) to 1.0 (deleterious). We prioritize max scores for MANE Select transcripts where possible and otherwise report a score for the canonical transcript.">
revel_max:
type:
- number
- 'null'
format: float
description: The maximum REVEL score at a site's MANE Select or canonical transcript. It's an ensemble score for predicting the pathogenicity of missense variants (based on 13 other variant predictors). Scores ranges from 0 to 1. Variants with higher scores are predicted to be more likely to be deleterious.">
sift_max:
type:
- number
- 'null'
format: float
description: Score reflecting the scaled probability of the amino acid substitution being tolerated, ranging from 0 to 1. Scores below 0.05 are predicted to impact protein function. We prioritize max scores for MANE Select transcripts where possible and otherwise report a score for the canonical transcript.">
spliceai_ds_max:
type:
- number
- 'null'
format: float
description: Illumina's SpliceAI max delta score; interpreted as the probability of the variant being splice-altering.">
cadd_raw:
type:
- number
- 'null'
format: float
description: Raw CADD scores are interpretable as the extent to which the annotation profile for a given variant suggests that the variant is likely to be 'observed' (negative values) vs 'simulated' (positive values). Larger values are more deleterious.
cadd_phred:
type:
- number
- 'null'
format: float
description: Cadd Phred-like scores ('scaled C-scores') ranging from 1 to 99, based on the rank of each variant relative to all possible 8.6 billion substitutions in the human reference genome. Larger values are more deleterious.
Gnomad4Record:
type: object
description: |-
Protocol buffer for the gnomAD-nuclear VCF record.
The more specialized fields from the INFO column are stored in separate, optional fields such
that we don't end up with a humongous message.
required:
- chrom
- pos
- ref_allele
- alt_allele
- filters
- vep
- allele_counts
- nonpar
- only_het
- outside_broad_capture_region
- outside_ukb_capture_region
- sibling_singleton
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: Alternate allele.
filters:
type: array
items:
$ref: '#/components/schemas/Gnomad3Filter'
description: Site-level filters.
vep:
type: array
items:
$ref: '#/components/schemas/Gnomad4Vep'
description: VEP annotation records.
allele_counts:
type: array
items:
$ref: '#/components/schemas/Gnomad4CohortAlleleCounts'
description: |-
Variant allele counts in the different cohorts and population.
The populations in gnomAD v4 are: empty for global, "joint" for exome+genomes.
nonpar:
type: boolean
description: Variant (on sex chromosome) falls outside a pseudoautosomal region
only_het:
type: boolean
description: All samples are heterozygous for the variant
outside_broad_capture_region:
type: boolean
description: Variant falls outside of Broad exome capture regions (exomes only).
outside_ukb_capture_region:
type: boolean
description: Variant falls outside of UK Biobank exome capture regions(exomes only).
sibling_singleton:
type: boolean
description: Variant was a callset-wide doubleton that was present only in two siblings (i.e., a singleton amongst unrelated samples in cohort) (exomes only).
effect_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad4EffectInfo'
description: Information on variant scores.
variant_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3VariantInfo'
description: Variant-related information details.
quality_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3QualityInfo'
description: Summary information for variant quality interpretation.
age_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3AgeInfo'
description: Age-related information.
depth_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad3DepthInfo'
description: Depth of coverage-related information.
vrs_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Gnomad4VrsInfo'
description: VRS infos.
Gnomad4Vep:
type: object
description: Protocol buffer for the gnomAD-nuclear VEP predictions.
required:
- allele
- consequence
- impact
- symbol
- gene
- feature_type
- feature
- feature_biotype
- domains
properties:
allele:
type: string
description: Allele of record.
consequence:
type: string
description: Consequence, e.g., `"missense_variant"`.
impact:
type: string
description: Impact, e.g., `"MODERATE"`.
symbol:
type: string
description: Gene symbol, e.g., `"PCSK9"`.
gene:
type: string
description: Gene ID, `e.g., "ENSG00000169174"`.
feature_type:
type: string
description: Feature type, e.g., `"Transcript"`.
feature:
type: string
description: Feature ID, e.g., `"ENST00000302118"`.
feature_biotype:
type: string
description: Feature biotype, e.g., `"protein_coding"`.
exon:
type:
- string
- 'null'
description: Ranked exon number, e.g., `"1/4"`.
intron:
type:
- string
- 'null'
description: Ranked intron number, e.g., `"1/4"`.
hgvsc:
type:
- string
- 'null'
description: cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`.
hgvsp:
type:
- string
- 'null'
description: Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`.
cdna_position:
type:
- string
- 'null'
description: cDNA position, e.g., `"89/1863"`.
cds_position:
type:
- string
- 'null'
description: CDS position, e.g., `"89/1863"`.
protein_position:
type:
- string
- 'null'
description: Protein position, e.g., `"30/620"`.
amino_acids:
type:
- string
- 'null'
description: Amino acids, e.g., `"T/R"`.
codons:
type:
- string
- 'null'
description: Codons, e.g., `"gCg/gGg"`.
allele_num:
type:
- integer
- 'null'
format: int32
description: Allele count.
distance:
type:
- string
- 'null'
description: Distance output of VEP.
strand:
type:
- string
- 'null'
description: Strand, e.g., `"1"`.
flags:
type:
- string
- 'null'
description: Flags
variant_class:
type:
- string
- 'null'
description: Variant class, e.g., `"SNV"`.
symbol_source:
type:
- string
- 'null'
description: Symbol source, e.g., `"HGNC"`.
hgnc_id:
type:
- string
- 'null'
description: HGNC ID, e.g., `"HGNC:8706"`.
canonical:
type:
- boolean
- 'null'
description: Whether this is the canonical transcript.
mane_select:
type:
- boolean
- 'null'
description: Presence in MANE Select
mane_plus_clinical:
type:
- boolean
- 'null'
description: Presence in MANE Plus Clinical
tsl:
type:
- integer
- 'null'
format: int32
description: Transcript support level, e.g., `"1"`.
appris:
type:
- string
- 'null'
description: APPRIS annotation, e.g. `"P1"`.
ccds:
type:
- string
- 'null'
description: CCDS ID, e.g., `"CCDS30547.1"`.
ensp:
type:
- string
- 'null'
description: Ensembl protein ID, e.g., `"ENSP00000302118"`.
uniprot_isoform:
type:
- string
- 'null'
description: Uniprot isoform.
source:
type:
- string
- 'null'
description: Value of VEP "SOURCE" field.
domains:
type: array
items:
$ref: '#/components/schemas/VepCommonDomain'
description: Protein domains, e.g., `\[["2p4e", "ENSP_mappings"\], \["2qtw", "ENSP_mappings"]\]`.
mirna:
type:
- string
- 'null'
description: miRNA information.
hgvs_offset:
type:
- string
- 'null'
description: HGVS offset.
pubmed:
type:
- string
- 'null'
description: PubMed IDs
motif_name:
type:
- string
- 'null'
description: Motif name.
motif_pos:
type:
- string
- 'null'
description: Motif name.
high_inf_pos:
type:
- string
- 'null'
description: '"high inf pos" from VEP.'
motif_score_change:
type:
- string
- 'null'
description: Motif score change.
transcription_factors:
type:
- string
- 'null'
description: Transcription factors.
lof:
type:
- string
- 'null'
description: Loss of function prediction.
lof_filter:
type:
- string
- 'null'
description: Loss of function filter.
lof_flags:
type:
- string
- 'null'
description: Loss of function flags.
lof_info:
type:
- string
- 'null'
description: Loss of function info.
Gnomad4VrsInfo:
type: object
description: VRS information
required:
- allele_ids
- ends
- starts
- states
properties:
allele_ids:
type: array
items:
type: string
description: The computed identifiers for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields
ends:
type: array
items:
type: integer
format: int32
description: Interresidue coordinates used as the location ends for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields
starts:
type: array
items:
type: integer
format: int32
description: Interresidue coordinates used as the location starts for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields
states:
type: array
items:
type: string
description: The literal sequence states used for the GA4GH VRS Alleles corresponding to the values in the REF and ALT fields
GnomadMtdnaAgeInfo:
type: object
description: Encapsulate VCF INFO fields related to age.
required:
- age_hist_hom_bin_freq
- age_hist_het_bin_freq
properties:
age_hist_hom_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a homoplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0].
age_hist_hom_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_hom_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
homoplasmic variant.
age_hist_het_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of ages of individuals with a heteroplasmic variant; bin edges are: [30.0, 35.0,
40.0, 45.0, 50.0, 55.0, 60.0, 65.0, 70.0, 75.0, 80.0]
age_hist_het_n_smaller:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling below lowest histogram bin edge for individuals with a
heteroplasmic variant.
age_hist_het_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of age values falling above highest histogram bin edge for individuals with a
heteroplasmic variant.
GnomadMtdnaDepthInfo:
type: object
description: Encapsulate VCF INFO fields related to depth.
required:
- dp_hist_all_bin_freq
- dp_hist_alt_bin_freq
properties:
dp_hist_all_n_larger:
type:
- integer
- 'null'
format: int32
description: Count of dp values falling above highest histogram bin edge for all individuals.
dp_hist_alt_n_larger:
type:
- integer
- 'null'
format: int32
description: |-
Count of dp values falling above highest histogram bin edge for individuals with the
alternative allele
dp_hist_all_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for all individuals; bin edges are: [0.0, 200.0, 400.0, 600.0, 800.0,
1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
dp_hist_alt_bin_freq:
type: array
items:
type: integer
format: int32
description: |-
Histogram of dp values for individuals with the alternative allele; bin edges are: [0.0,
200.0, 400.0, 600.0, 800.0, 1000.0, 1200.0, 1400.0, 1600.0, 1800.0, 2000.0]
GnomadMtdnaFilter:
type: string
description: Protocol buffer enum for site-level filters.
enum:
- artifact_prone_site
- indel_stack
- no_pass_genotype
GnomadMtdnaFilterHistograms:
type: object
description: Encapsulate VCF INFO fields related to filter failure histograms.
required:
- base_qual_hist
- position_hist
- strand_bias_hist
- weak_evidence_hist
- contamination_hist
properties:
base_qual_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals failing the base_qual filter (alternate allele median base
quality) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4,
0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0]
position_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals failing the position filter (median distance of alternate
variants from end of reads) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2, 0.
30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0]
strand_bias_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals failing the strand_bias filter (evidence for alternate
allele comes from one read direction only) across heteroplasmy levels, bin edges are: [0.0,
0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9,
1.0]
weak_evidence_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals failing the weak_evidence filter (mutation does not meet
likelihood threshold) across heteroplasmy levels, bin edges are: [0.0, 0.1, 0.2,
0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0]
contamination_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals failing the contamination filter across heteroplasmy
levels, bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001,
0.7000000000000001, 0.8, 0.9, 1.0]
GnomadMtdnaHaplogroupInfo:
type: object
description: Encapsulate VCF INFO fields related to haplogroups.
required:
- hap_defining_variant
- hap_an
- hap_ac_het
- hap_ac_hom
- hap_af_het
- hap_af_hom
- hap_hl_hist
- hap_faf_hom
properties:
hap_defining_variant:
type: boolean
description: Present if variant is present as a haplogroup defining variant in PhyloTree build 17.
hap_an:
type: array
items:
type: integer
format: int32
description: |-
List of overall allele number for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D',
'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P',
'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']
hap_ac_het:
type: array
items:
type: integer
format: int32
description: |-
List of AC_het for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U',
'V', 'W', 'X', 'Y', 'Z']
hap_ac_hom:
type: array
items:
type: integer
format: int32
description: |-
List of AC_hom for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U',
'V', 'W', 'X', 'Y', 'Z']
hap_af_het:
type: array
items:
type: number
format: float
description: |-
List of AF_het for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U',
'V', 'W', 'X', 'Y', 'Z']
hap_af_hom:
type: array
items:
type: number
format: float
description: |-
List of AF_hom for each haplogroup, haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G',
'H', 'HV', 'I', 'J', 'K', 'L0', 'L1', 'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U',
'V', 'W', 'X', 'Y', 'Z']
hap_hl_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of heteroplasmy levels for each haplogroup; bin edges are: [0.0, 0.1, 0.2,
0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0],
haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1',
'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']
Note that we encode this by concatenating all lists here because of limitations in
protocolbuffers (no native nested repeated fields).
hap_faf_hom:
type: array
items:
type: number
format: float
description: |-
List of filtering allele frequency for each haplogroup restricted to homoplasmic variants,
haplogroup order: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'HV', 'I', 'J', 'K', 'L0', 'L1',
'L2', 'L3', 'L4', 'L5', 'M', 'N', 'P', 'R', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']
hapmax_af_hom:
type:
- string
- 'null'
description: Haplogroup with maximum AF_hom.
hapmax_af_het:
type:
- string
- 'null'
description: Haplogroup with maximum AF_het.
faf_hapmax_hom:
type:
- number
- 'null'
format: float
description: Maximum filtering allele frequency across haplogroups restricted to homoplasmic variants.
GnomadMtdnaHeteroplasmyInfo:
type: object
description: Encapsulate VCF INFO fields related to heteroplasmy levels.
required:
- heteroplasmy_below_min_het_threshold_hist
- hl_hist
- common_low_heteroplasmy
- max_hl
properties:
heteroplasmy_below_min_het_threshold_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of number of individuals with a heteroplasmy level below 0.1, bin edges are: [0.0,
0.1, 0.2, 0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9,
1.0]
hl_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of heteroplasmy levels; bin edges are: [0.0, 0.1, 0.2, 0.30000000000000004, 0.4,
0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0].
common_low_heteroplasmy:
type: boolean
description: |-
Present if variant is found at an overall frequency of .001 across all samples with a
heteroplasmy level > 0 and < 0.50 (includes variants <0.01 heteroplasmy which are
subsequently filtered)
max_hl:
type: number
format: float
description: Maximum heteroplasmy level observed among all samples for that variant.
GnomadMtdnaPopulationInfo:
type: object
description: Encapsulate VCF INFO fields related to populations.
required:
- pop_an
- pop_ac_het
- pop_ac_hom
- pop_af_hom
- pop_af_het
- pop_hl_hist
properties:
pop_an:
type: array
items:
type: integer
format: int32
description: |-
List of overall allele number for each population, population order: ['afr', 'ami', 'amr',
'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid']
pop_ac_het:
type: array
items:
type: integer
format: int32
description: |-
List of AC_het for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas',
'fin', 'nfe', 'oth', 'sas', 'mid']
pop_ac_hom:
type: array
items:
type: integer
format: int32
description: |-
List of AC_hom for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas',
'fin', 'nfe', 'oth', 'sas', 'mid']
pop_af_hom:
type: array
items:
type: number
format: float
description: |-
List of AF_hom for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas',
'fin', 'nfe', 'oth', 'sas', 'mid']
pop_af_het:
type: array
items:
type: number
format: float
description: |-
List of AF_het for each population, population order: ['afr', 'ami', 'amr', 'asj', 'eas',
'fin', 'nfe', 'oth', 'sas', 'mid']
pop_hl_hist:
type: array
items:
type: integer
format: int32
description: |-
Histogram of heteroplasmy levels for each population; bin edges are: [0.0, 0.1, 0.2,
0.30000000000000004, 0.4, 0.5, 0.6000000000000001, 0.7000000000000001, 0.8, 0.9, 1.0],
population order: \['afr', 'ami', 'amr', 'asj', 'eas', 'fin', 'nfe', 'oth', 'sas', 'mid'\]
Note that we encode this by concatenating all lists here because of limitations in
protocolbuffers (no native nested repeated fields).
GnomadMtdnaQualityInfo:
type: object
description: Encapsulate VCF INFO fields related to quality.
properties:
dp_mean:
type:
- number
- 'null'
format: float
description: Mean depth across all individuals for the site.
mq_mean:
type:
- number
- 'null'
format: float
description: Mean MMQ (median mapping quality) across individuals with a variant for the site.
tlod_mean:
type:
- number
- 'null'
format: float
description: |-
Mean TLOD (Log 10 likelihood ratio score of variant existing versus not existing) across
individuals with a variant for the site.
GnomadMtdnaRecord:
type: object
description: |-
Protocol buffer for the gnomAD-mtDNA VCF record.
The more specialized fields from the INFO column are stored in separate, optional fields such
that we don't end up with a humongous message.
required:
- chrom
- pos
- ref_allele
- alt_allele
- variant_collapsed
- excluded_ac
- an
- ac_hom
- ac_het
- af_hom
- af_het
- filters
- vep
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: Alternate allele.
variant_collapsed:
type: string
description: Variant in format of RefPosAlt
excluded_ac:
type: integer
format: int32
description: Excluded allele count (number of individuals in which the variant was filtered out).
an:
type: integer
format: int32
description: Overall allele number (number of samples with non-missing genotype).
ac_hom:
type: integer
format: int32
description: Allele count restricted to variants with a heteroplasmy level >= 0.95.
ac_het:
type: integer
format: int32
description: Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95.
af_hom:
type: number
format: float
description: Allele frequency restricted to variants with a heteroplasmy level >= 0.95.
af_het:
type: number
format: float
description: Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95.
filters:
type: array
items:
$ref: '#/components/schemas/GnomadMtdnaFilter'
description: Site-level filters.
mitotip_score:
type:
- number
- 'null'
format: float
description: MitoTip raw score
mitotip_trna_prediction:
type:
- string
- 'null'
description: MitoTip score interpretation
pon_mt_trna_prediction:
type:
- string
- 'null'
description: tRNA pathogenicity classification from PON-mt-tRNA
pon_ml_probability_of_pathogenicity:
type:
- string
- 'null'
description: tRNA ML_probability_of_pathogenicity from PON-mt-tRNA
vep:
type: array
items:
$ref: '#/components/schemas/Gnomad3Vep'
description: VEP v3 annotation records.
quality_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaQualityInfo'
description: Summary information for variant quality interpretation.
heteroplasmy_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaHeteroplasmyInfo'
description: Information related to heteroplasmy levels.
filter_histograms:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaFilterHistograms'
description: Histograms related to variant quality filters.
population_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaPopulationInfo'
description: Population-related information.
haplogroup_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaHaplogroupInfo'
description: Haplogroup-related information.
age_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaAgeInfo'
description: Age-related information.
depth_info:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaDepthInfo'
description: Depth of coverage-related information.
GnomadRecord:
oneOf:
- type: object
description: gnomAD v2 record.
required:
- gnomad2
properties:
gnomad2:
$ref: '#/components/schemas/Gnomad2Record'
description: gnomAD v2 record.
- type: object
description: gnomAD v3 record.
required:
- gnomad3
properties:
gnomad3:
$ref: '#/components/schemas/Gnomad3Record'
description: gnomAD v3 record.
- type: object
description: gnomAD v4 record.
required:
- gnomad4
properties:
gnomad4:
$ref: '#/components/schemas/Gnomad4Record'
description: gnomAD v4 record.
description: Allow either a gnomAD v2/v3 or v4 record.
HelixMtDbRecord:
type: object
description: A HelixMtDb record.
required:
- chrom
- pos
- ref_allele
- alt_allele
- num_total
- num_het
- num_hom
- feature_type
- gene_name
properties:
chrom:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based start position.
ref_allele:
type: string
description: Reference allele.
alt_allele:
type: string
description: / Alternate allele.
num_total:
type: integer
format: int32
description: Total number of individuals.
num_het:
type: integer
format: int32
description: Number of homoplasmic carriers.
num_hom:
type: integer
format: int32
description: Number of heteroplasmic carriers.
feature_type:
type: string
description: Feature type.
gene_name:
type: string
description: Gene name.
Scored:
type: object
description: A scored result.
required:
- score
- data
properties:
score:
type: number
format: float
description: The score.
data:
$ref: '#/components/schemas/GeneNames'
description: The result.
SeqvarsAnnoResponseRecord:
type: object
description: Annotation for a sinngle variant.
properties:
cadd:
type:
- object
- 'null'
description: Annotations from CADD (TSV annotation file).
additionalProperties: {}
propertyNames:
type: string
dbsnp:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/DbsnpRecord'
description: Annotations from dbSNP.
dbnsfp:
type:
- object
- 'null'
description: Annotations from dbNSFP (TSV annotation file).
additionalProperties: {}
propertyNames:
type: string
dbscsnv:
type:
- object
- 'null'
description: Annotations from dbscSNV.
additionalProperties: {}
propertyNames:
type: string
gnomad_mtdna:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadMtdnaRecord'
description: Annotations from gnomAD-mtDNA.
gnomad_exomes:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadRecord'
description: Annotations from gnomAD-exomes.
gnomad_genomes:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/GnomadRecord'
description: Annotations from gnomAD-genomes.
helixmtdb:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/HelixMtDbRecord'
description: Annotations from HelixMTdb.
ucsc_conservation:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/UcscConservationRecordList'
description: Annotations from UCSC conservation.
clinvar:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ExtractedVcvRecordList'
description: Minimal extracted data from ClinVar.
SeqvarsAnnosQuery:
type: object
description: |-
Parameters for `variant_annos::handle`.
Defines a variant in VCF-style format with a genome release specification.
required:
- genome_release
- chromosome
- pos
- reference
- alternative
properties:
genome_release:
type: string
description: Genome release specification.
chromosome:
type: string
description: Chromosome name.
pos:
type: integer
format: int32
description: 1-based position for VCF-style variant.
minimum: 0
reference:
type: string
description: Reference allele bases.
alternative:
type: string
description: Alterantive allele bases.
SeqvarsAnnosResponse:
type: object
description: Query response for `handle_with_openapi()`.
required:
- result
properties:
result:
$ref: '#/components/schemas/SeqvarsAnnoResponseRecord'
description: The result records.
StrucvarsClinvarPageInfo:
type: object
description: Information regarding the pagination.
required:
- total
- per_page
- current_page
- total_pages
properties:
total:
type: integer
format: int32
description: The total number of records.
minimum: 0
per_page:
type: integer
format: int32
description: The number of records per page.
minimum: 0
current_page:
type: integer
format: int32
description: The current page number.
minimum: 0
total_pages:
type: integer
format: int32
description: The total number of pages.
minimum: 0
StrucvarsClinvarQuery:
type: object
description: Query of the `/api/v1/strucvars/clinvar-annos/query` endpoint.
required:
- genome_release
- chromosome
- start
- stop
properties:
genome_release:
$ref: '#/components/schemas/GenomeRelease'
description: Genome release specification.
chromosome:
type: string
description: Chromosome name.
start:
type: integer
format: int32
description: 1-based start position.
minimum: 0
stop:
type: integer
format: int32
description: 1-based stop postion.
minimum: 0
variation_types:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/ClinvarExtractedVariationType'
description: Optionally, the variant types.
min_overlap:
type:
- number
- 'null'
format: double
description: Optionally, minimal overlap.
page_no:
type:
- integer
- 'null'
format: int32
description: Optional 1-based page number.
minimum: 0
page_size:
type:
- integer
- 'null'
format: int32
description: Optional page size.
minimum: 0
StrucvarsClinvarResponse:
type: object
description: Response of the `/api/v1/strucvars/clinvar-annos/query` endpoint.
required:
- records
- page_info
properties:
records:
type: array
items:
$ref: '#/components/schemas/StrucvarsClinvarResponseRecord'
description: The records in this page.
page_info:
$ref: '#/components/schemas/StrucvarsClinvarPageInfo'
description: Pagination information.
StrucvarsClinvarResponseRecord:
type: object
description: Information on one response record.
required:
- overlap
properties:
record:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/ClinvarExtractedVcvRecord'
description: The record.
overlap:
type: number
format: double
description: The reciprocal overlap with the query.
UcscConservationRecord:
type: object
description: A UCSC conservation record.
required:
- chrom
- start
- stop
- hgnc_id
- enst_id
- exon_num
- exon_count
- alignment
properties:
chrom:
type: string
description: Chromosome name.
start:
type: integer
format: int32
description: 1-based, inclusive start position.
stop:
type: integer
format: int32
description: 1-based, inclusive stop position.
hgnc_id:
type: string
description: HGNC identifier.
enst_id:
type: string
description: ENST identifier.
exon_num:
type: integer
format: int32
description: Exon number (1-based).
exon_count:
type: integer
format: int32
description: Exon count.
alignment:
type: string
description: Alignment.
UcscConservationRecordList:
type: object
description: List of `Record`s.
required:
- records
properties:
records:
type: array
items:
$ref: '#/components/schemas/UcscConservationRecord'
description: The records in the list.
VepCommonDomain:
type: object
description: Protocol buffer for `Vep.domains`
required:
- id
- source
properties:
id:
type: string
description: Domain ID.
source:
type: string
description: Domain source.
VepCommonPrediction:
type: object
description: Store the scoring of a prediction.
required:
- prediction
- score
properties:
prediction:
type: string
description: Prediction.
score:
type: number
format: float
description: Score.
VersionsAnnotationInfo:
type: object
description: Version information for one database.
required:
- database
properties:
database:
$ref: '#/components/schemas/AnnoDb'
description: Database name.
version_spec:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VersionsVersionSpec'
description: Version information of the database.
VersionsCreatedFrom:
type: object
description: Source name and version.
required:
- name
- version
properties:
name:
type: string
description: The name of the data source.
version:
type: string
description: The version of the data source.
VersionsInfoQuery:
type: object
description: Query parameters for `handle()`.
VersionsInfoResponse:
type: object
description: Response for `handle()`.
properties:
genes:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/VersionsVersionSpec'
description: Version information of the genes.
seqvars:
type: array
items:
$ref: '#/components/schemas/VersionsPerRelease'
description: Version information of annotation databases per release.
VersionsPerRelease:
type: object
description: Version information for databases in a given release.
required:
- release
properties:
release:
$ref: '#/components/schemas/GenomeRelease'
description: The genome release.
version_infos:
type: array
items:
$ref: '#/components/schemas/VersionsAnnotationInfo'
description: Version information of annotation databases.
VersionsVersionSpec:
type: object
description: Version specification.
required:
- identifier
- title
- creator
- contributor
- format
- date
- version
- description
- source
- created_from
properties:
identifier:
type: string
description: Identifier of the data.
title:
type: string
description: Title of the data.
creator:
type: string
description: Creator of the data.
contributor:
type: array
items:
type: string
description: Contributors of the data.
format:
type: string
description: Format of the data.
date:
type: string
description: Date of the data.
version:
type: string
description: Version of the data.
genome_release:
type:
- string
- 'null'
description: Optional genome release.
description:
type: string
description: Data description.
source:
type: array
items:
type: string
description: Data source.
created_from:
type: array
items:
$ref: '#/components/schemas/VersionsCreatedFrom'
description: Created from information.