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gnomad-database

Retrieve gnomAD allele frequencies and gene constraint metrics via GraphQL.

2.7k|283|Updated May 13, 2026
Search Tags:#genomics#graphql api#gnomad#variant frequency#gene constraint#loss-of-function
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill gnomad-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill gnomad-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scienceskillscommon, and includes scripts (resource) components.

What problem does it solve?

Determining how rare a genetic variant is and what gene-level constraint implies can be time-consuming when you need reliable allele frequency and constraint metrics.

Core Features & Use Cases

  • Variant allele frequency queries (global, ancestry-specific): Look up allele counts, allele frequencies, homozygote/hemizygote counts, and Grpmax filtering allele frequency (faf95/faf99) for exome, genome, or joint data.
  • Gene constraint retrieval: Fetch pLI and LOEUF-style constraint metrics (including oe_lof_upper) for loss-of-function intolerance assessment.
  • Region/gene variant search: Find variants in a genomic region or within a gene, with optional filtering by consequence such as pLoF or missense.

Quick Start

Use the provided scripts to query gnomAD for a variant’s frequency by running: uv run /path/to/gnomad_database/scripts/get_variant_frequency.py --variant_id 1-55516888-G-GA --dataset gnomad_r4 --output variant_frequency.json.

Frequently Asked Questions about gnomad-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I look up gnomAD allele frequency for a specific genetic variant?▼

To look up gnomAD allele frequency, use the provided wrapper scripts to query the GraphQL API with a variant ID and dataset, retrieving allele counts, homozygote counts, and filtering allele frequency metrics.

How do I get pLI and LOEUF gene constraint metrics for loss-of-function intolerance?▼

Retrieve pLI and LOEUF-style constraint metrics by querying gnomAD gene constraint data, which provides loss-of-function intolerance scores like oe_lof_upper for assessing gene essentiality.

Can I find all loss-of-function variants within a specific gene or genomic region in gnomAD?▼

Yes, you can find variants within a gene or genomic region by querying gnomAD, applying optional filtering by consequence such as pLoF or missense to narrow the search results.

Does querying gnomAD variant data require using specific scripts to handle rate limits?▼

Yes, querying gnomAD requires using the provided wrapper scripts, which enforce gnomAD usage policies via a built-in rate-limited HTTP GraphQL client to ensure compliant data retrieval.

Can I retrieve ancestry-specific allele frequencies from gnomAD exome and genome datasets?▼

Yes, gnomAD allele frequency queries support retrieving global and ancestry-specific data, including allele counts and frequencies across exome, genome, or joint datasets.

What is the difference between gnomAD faf95 and faf99 filtering allele frequencies?▼

Grpmax filtering allele frequencies like faf95 and faf99 are metrics retrieved from gnomAD queries to help assess variant rarity while mitigating ancestry population structure effects.

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