107 lines
3.3 KiB
Markdown
107 lines
3.3 KiB
Markdown
---
|
|
title: "gnomAD (Genome Aggregation Database) API Reference"
|
|
task: ""
|
|
lineage_type: import
|
|
upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/gnomad.md
|
|
upstream_sha: 9c9bd2e9
|
|
imported_at: 2026-06-26
|
|
prompt_class: prompt
|
|
upstream_changes: accepted
|
|
author: upstream
|
|
validated: 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
|
|
```json
|
|
{
|
|
"query": "{ gene(gene_symbol: \"BRCA1\", reference_genome: GRCh38) { gene_id symbol chrom start stop strand } }"
|
|
}
|
|
```
|
|
|
|
### Variants in a gene
|
|
```json
|
|
{
|
|
"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
|
|
```json
|
|
{
|
|
"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
|
|
```json
|
|
{
|
|
"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)
|
|
```json
|
|
{
|
|
"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`
|