Pure.
AlphaMissense is nested
It is at transcript_consequences[].alphamissense$am_pathogenicity, per
transcript. There is nothing at the top level. Hoisting the read out of the
transcript is the single easiest way to get NA everywhere and conclude the
API does not serve it.
Optional columns
hgvsc, hgvsp, canonical, cadd_phred, cadd_raw, revel, the
spliceai_* scores and lof are only populated when the matching flag was
requested, see vep_default_options(). Otherwise they are NA. VEP marks
only the canonical transcript, so canonical is TRUE on that transcript
and NA everywhere else, including when the flag was never asked.
spliceai_max is the largest of the four SpliceAI delta scores.
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(
gene_symbol = "BRAF", consequence_terms = list("missense_variant"),
alphamissense = list(am_pathogenicity = 0.99, am_class = "pathogenic")
))
)
vep_parse_element(element)
#> # A tibble: 1 × 27
#> gene consequence mane impact exon protein_pos sift polyphen alphamissense
#> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <dbl>
#> 1 BRAF missense_va… NA NA NA NA NA NA 0.99
#> # ℹ 18 more variables: alphamissense_class <chr>, transcript <chr>,
#> # gene_id <chr>, biotype <chr>, hgvsc <chr>, hgvsp <chr>, canonical <lgl>,
#> # codons <chr>, amino_acids <chr>, cadd_phred <dbl>, cadd_raw <dbl>,
#> # revel <dbl>, spliceai_ds_ag <dbl>, spliceai_ds_al <dbl>,
#> # spliceai_ds_dg <dbl>, spliceai_ds_dl <dbl>, spliceai_max <dbl>, lof <chr>