Population allele frequency for a variant, by id

Looked up by chrom-pos-ref-alt, which names one allele exactly. This is the lookup gnomad_frequency() cannot do, because an rsID is shared by every allele at a site.

Usage

gnomad_frequency_by_id(
  variant_id,
  dataset = GNOMAD_DATASET,
  reference_genome = "GRCh38",
  ...
)

Arguments

variant_id

A gnomAD variant id, see gnomad_variant_id().

dataset

The gnomAD dataset. gnomad_r4 is GRCh38; the gnomad_r2 datasets are GRCh37.

reference_genome

The assembly the id is on. The variant query is keyed by dataset alone, so this is checked against dataset and a mismatch is refused rather than sent, because gnomAD would answer with whatever sits at those coordinates on the other assembly.

...

Passed to biohttp::post_json().

Value

A biohttp envelope whose data is the one-row tibble described in gnomad_parse_variant(). no_data when gnomAD has no record of the variant.

References

Chen et al. (2024). A genomic mutational constraint map using variation in 76,156 human genomes. Nature 625(7993), 92-100. doi:10.1038/s41586-023-06045-0

Service documentation: https://gnomad.broadinstitute.org/

Examples

# \donttest{
biohttp::body_or_null(gnomad_frequency_by_id("17-7676154-G-C"))
#> # A tibble: 1 × 16
#>   variant_id  rsid  exome_af exome_ac exome_an exome_nhomalt genome_af genome_ac
#>   <chr>       <chr>    <dbl>    <dbl>    <dbl>         <dbl>     <dbl>     <dbl>
#> 1 17-7676154… rs10…    0.716  1046941  1461558        380188     0.627     95285
#> # ℹ 8 more variables: genome_an <dbl>, genome_nhomalt <dbl>, grpmax_af <dbl>,
#> #   grpmax_an <dbl>, grpmax_id <chr>, faf95 <dbl>, faf95_pop <chr>,
#> #   filters <chr>
# }