This function retrieves variant consequence types. For more details check Ensembl Variation - Calculated variant consequences.
Value
A tibble, each row being a variant consequence,
of four variables:
- SO_accession
Sequence Ontology accession, e.g.,
'SO:0001626'.- SO_term
Sequence Ontology term, e.g.,
'incomplete_terminal_codon_variant'.- label
Display term.
- description
Sequence Ontology description.
Details
A rule-based approach is used to predict the effects that each allele of a variant may have on each transcript. These effects are variant consequences, that are catalogued as consequence terms, defined by the Sequence Ontology.
See below a diagram showing the location of each display term relative to the transcript structure:
Ensembl REST API endpoints
get_variant_consequence_types makes GET requests to
/info/variation/consequence_types.
Examples
# Retrieve variant consequence types
get_variant_consequences()
#> # A tibble: 41 × 4
#> SO_accession SO_term label description
#> <chr> <chr> <chr> <chr>
#> 1 SO:0001627 intron_variant intron variant A transcri…
#> 2 SO:0001819 synonymous_variant synonymous variant A sequence…
#> 3 SO:0001567 stop_retained_variant stop retained varia… A sequence…
#> 4 SO:0001060 sequence_variant sequence variant A sequence…
#> 5 SO:0001822 inframe_deletion inframe deletion An inframe…
#> 6 SO:0001891 regulatory_region_amplification regulatory region a… A feature …
#> 7 SO:0001787 splice_donor_5th_base_variant splice donor 5th ba… A sequence…
#> 8 SO:0001889 transcript_amplification transcript amplific… A feature …
#> 9 SO:0001968 coding_transcript_variant coding transcript v… A transcri…
#> 10 SO:0001624 3_prime_UTR_variant 3 prime UTR variant A UTR vari…
#> # ℹ 31 more rows