drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/gnomad.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
gnomAD (Genome Aggregation Database) API Reference		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/gnomad.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

gnomAD (Genome Aggregation Database) API Reference

Overview

gnomAD aggregates exome and genome sequencing data to provide allele frequencies and variant annotations across diverse populations.

API Type: GraphQL

• Endpoint: https://gnomad.broadinstitute.org/api
• Method: POST with JSON body containing GraphQL query
• Auth: None required (public, unauthenticated)
• Response format: JSON (data wrapper with GraphQL structure)

Key Queries

Variant lookup by variant ID

Variant IDs use format: {chrom}-{pos}-{ref}-{alt} (GRCh37 or GRCh38).

POST https://gnomad.broadinstitute.org/api
Content-Type: application/json

{
  "query": "{ variant(variantId: \"1-55516888-G-A\", dataset: gnomad_r4) { variant_id rsids chrom pos ref alt exome { ac an af } genome { ac an af } } }"
}

Gene lookup

{
  "query": "{ gene(gene_symbol: \"BRCA1\", reference_genome: GRCh38) { gene_id symbol chrom start stop strand } }"
}

Variants in a gene

{
  "query": "{ gene(gene_symbol: \"PCSK9\", reference_genome: GRCh38) { variants(dataset: gnomad_r4) { variant_id consequence rsids exome { ac an af } genome { ac an af } } } }"
}

Variants in a region

{
  "query": "{ region(chrom: \"1\", start: 55505222, stop: 55530526, reference_genome: GRCh38) { variants(dataset: gnomad_r4) { variant_id rsids consequence exome { ac af } genome { ac af } } } }"
}

Transcript lookup

{
  "query": "{ transcript(transcript_id: \"ENST00000357654\", reference_genome: GRCh38) { transcript_id gene_id chrom start stop strand } }"
}

Dataset values

• gnomad_r4 -- gnomAD v4 (GRCh38, latest major release)
• gnomad_r3 -- gnomAD v3.1.2 (GRCh38, genomes only)
• gnomad_r2_1 -- gnomAD v2.1.1 (GRCh37, exomes + genomes)

Population frequency fields

Within exome or genome objects, population-specific frequencies are available via populations { id ac an af } where id values include: afr, amr, asj, eas, fin, mid, nfe, oth, sas.

Response example (variant)

{
  "data": {
    "variant": {
      "variant_id": "1-55516888-G-A",
      "rsids": ["rs11591147"],
      "chrom": "1",
      "pos": 55516888,
      "ref": "G",
      "alt": "A",
      "exome": { "ac": 1234, "an": 250000, "af": 0.004936 },
      "genome": { "ac": 456, "an": 150000, "af": 0.00304 }
    }
  }
}

Rate Limits

• No published rate limits, but aggressive querying will be throttled
• Use reasonable request pacing (~1 req/sec recommended)
• For bulk downloads, use gnomAD's Hail tables on Google Cloud or download VCFs

Notes

• The GraphQL schema is not versioned separately; it tracks the gnomAD web interface
• Use the browser's network inspector on gnomad.broadinstitute.org to discover additional query fields and structures
• Structural variants (SV) have a separate query structure (structural_variant)
• Constraint metrics (pLI, LOEUF) are available on gene queries via gnomad_constraint