gnomAD¶
gnomAD is the quickest way to answer the question that often changes an interpretation: how rare is this variant, and how constrained is this gene in population data? It matters because frequency and constraint are among the fastest filters for separating plausible signals from common background variation.
In BioMCP, gene constraint comes from the gnomAD source path directly, and
variant population data now does too. Variant population requests are pinned to
the gnomad_r4 dataset and require a trustworthy GRCh38 coordinate. This
replaces population fields previously copied from MyVariant.info payloads.
What BioMCP exposes¶
| Command | What BioMCP gets from this source | Integration note |
|---|---|---|
get gene <symbol> constraint |
Gene-level constraint metrics such as LOEUF-style context | Direct gnomAD-backed gene section |
get variant <id> population |
Compact exome/genome frequencies, highest observed population-row frequency with AC/AN, grpmax FAF95, and quality flags | Direct gnomad_r4 GraphQL query for the resolved GRCh38 coordinate |
get variant <id> population-details |
Full exome/genome ancestry tables | Uses the same direct gnomad_r4 result |
search variant -g <gene> --max-frequency <value> |
Rarity-filtered variant search rows | Search filter uses population-frequency context aligned with gnomAD fields |
Example commands¶
Returns a constraint section with gnomAD provenance and LOEUF-style metrics.
Returns compact direct gnomAD v4 exome and genome population results. For the highest observed population-row frequency, allele count (AC) is shown over allele number (AN). AN is the AF denominator: the number of alleles with a defined genotype call at that site, not a count of samples or people. JSON keeps raw numeric frequencies, counts, FAF95, ancestry rows, and source flag names.
biomcp get variant "chr7:g.140453136A>T" population
biomcp get variant "chr7:g.140453136A>T" population-details
The first command returns compact frequencies; the second returns full ancestry tables. A GRCh37-only or unknown-build result explains the requirement and does not query gnomAD.
Returns variant rows constrained by a rarity filter.
API access¶
No BioMCP API key required.
Official source¶
gnomAD is the official Broad Institute population-resource homepage behind these frequency and constraint views.