Enum Consequence 

pub enum Consequence {
    TranscriptAblation,
    SpliceAcceptorVariant,
    SpliceDonorVariant,
    StopGained,
    FrameshiftVariant,
    StopLost,
    StartLost,
    InframeInsertion,
    InframeDeletion,
    MissenseVariant,
    ProteinAlteringVariant,
    SpliceRegionVariant,
    StartRetainedVariant,
    StopRetainedVariant,
    IncompleteTerminalCodonVariant,
    SynonymousVariant,
    CodingSequenceVariant,
    FivePrimeUtrVariant,
    ThreePrimeUtrVariant,
    NonCodingTranscriptExonVariant,
    IntronVariant,
    UpstreamGeneVariant,
    DownstreamGeneVariant,
    IntergenicVariant,
}

Sequence Ontology consequence term with its VEP-assigned IMPACT.

The string representation (via Consequence::as_str) matches VEP’s output exactly (e.g., "missense_variant"). Covers SNV, indel, boundary-spanning, complex delins, and MNV consequence terms.

Variants

TranscriptAblation

Variant causes loss of the transcription unit (typically large SVs).

SpliceAcceptorVariant

Variant in the canonical splice acceptor site (intronic -1 or -2).

SpliceDonorVariant

Variant in the canonical splice donor site (intronic +1 or +2).

StopGained

Premature stop codon introduced by the variant.

FrameshiftVariant

Insertion or deletion shifts the reading frame (length change not divisible by 3).

StopLost

Stop codon changed to a coding amino acid.

StartLost

Start codon (ATG) disrupted – translation initiation site lost.

InframeInsertion

In-frame insertion of one or more codons (length divisible by 3).

InframeDeletion

In-frame deletion of one or more codons (length divisible by 3).

MissenseVariant

Non-synonymous coding change – different amino acid.

ProteinAlteringVariant

Coding variant whose exact protein effect is ambiguous (e.g. complex delins that changes both sequence and length).

SpliceRegionVariant

Variant in the splice region (intronic +3..+8 / -3..-8, or exonic 1-3 bases from boundary). Always paired with the primary consequence.

StartRetainedVariant

Synonymous change at the start codon (ATG preserved). Only possible on chrM where ATA also codes for Met (NCBI table 2).

StopRetainedVariant

Synonymous change within the stop codon.

IncompleteTerminalCodonVariant

SO:0001626 – variant in the final partial codon of an incompletely annotated CDS (total CDS length not divisible by 3).

SynonymousVariant

Synonymous coding change – same amino acid.

CodingSequenceVariant

Variant in a coding exon but codon could not be determined (e.g., reference contains N).

FivePrimeUtrVariant

Variant in the 5’ UTR.

ThreePrimeUtrVariant

Variant in the 3’ UTR.

NonCodingTranscriptExonVariant

Variant in an exon of a non-coding transcript.

IntronVariant

Variant in an intron.

UpstreamGeneVariant

Variant upstream of the transcript (within 5 kb, 5’ direction).

DownstreamGeneVariant

Variant downstream of the transcript (within 5 kb, 3’ direction).

IntergenicVariant

Variant does not overlap any transcript’s [tx_start, tx_end) region.

Implementations

impl Consequence

pub fn impact(&self) -> Impact

VEP’s IMPACT rating for this consequence.

pub fn severity_rank(&self) -> u8

Severity rank (lower = more severe). Matches VEP’s ordering.

pub fn as_str(&self) -> &'static str

SO term string as VEP would output it (e.g., "missense_variant").

Trait Implementations

impl Clone for Consequence

fn clone(&self) -> Consequence

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Consequence

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Hash for Consequence

fn hash<__H: Hasher>(&self, state: &mut __H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl Ord for Consequence

fn cmp(&self, other: &Consequence) -> Ordering

This method returns an Ordering between self and other.

fn max(self, other: Self) -> Self

where Self: Sized,

Compares and returns the maximum of two values.

fn min(self, other: Self) -> Self

where Self: Sized,

Compares and returns the minimum of two values.

fn clamp(self, min: Self, max: Self) -> Self

where Self: Sized,

Restrict a value to a certain interval.

impl PartialEq for Consequence

fn eq(&self, other: &Consequence) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl PartialOrd for Consequence

fn partial_cmp(&self, other: &Consequence) -> Option<Ordering>

This method returns an ordering between self and other values if one exists.

fn lt(&self, other: &Rhs) -> bool

Tests less than (for self and other) and is used by the < operator.

fn le(&self, other: &Rhs) -> bool

Tests less than or equal to (for self and other) and is used by the <= operator.

fn gt(&self, other: &Rhs) -> bool

Tests greater than (for self and other) and is used by the > operator.

fn ge(&self, other: &Rhs) -> bool

Tests greater than or equal to (for self and other) and is used by the >= operator.

impl Copy for Consequence

impl Eq for Consequence

impl StructuralPartialEq for Consequence