Choose which transcript to report for a variant

Pure. A variant hits many transcripts and only one row can be reported.

Usage

vep_pick_transcript(element)

Arguments

element

One parsed VEP result element.

Value

One transcript consequence, or NULL when there are none.

Details

The order is MANE Select first, because that is the community's designated representative transcript; then whichever transcript carries the variant's most severe consequence; then the first VEP listed. Taking the first outright reports an arbitrary transcript, often a non-coding one, which makes the consequence look milder than it is.

References

McLaren et al. (2016). The Ensembl Variant Effect Predictor. Genome Biology 17, 122. doi:10.1186/s13059-016-0974-4

Service documentation: https://rest.ensembl.org/

Examples

element <- list(
  most_severe_consequence = "missense_variant",
  transcript_consequences = list(
    list(consequence_terms = list("intron_variant")),
    list(consequence_terms = list("missense_variant"), mane_select = "NM_1")
  )
)
vep_pick_transcript(element)$mane_select
#> [1] "NM_1"