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gnomad-database

Query the gnomAD v4 GraphQL API for variant frequencies, gene constraint metrics, and coverage.

298|27|Updated Feb 18, 2026
Search Tags:#graphql#bioinformatics#gnomad#population genetics#variant frequency#gene constraint
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill gnomad-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/gnomad-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill gnomad-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill allows users to query the Genome Aggregation Database (gnomAD) to retrieve population variant frequencies, gene constraint metrics, and coverage data, enabling researchers to assess variant rarity and evolutionary constraint.

Core Features & Use Cases

  • Variant Frequency Lookup: Retrieve allele counts and frequencies for specific variants across multiple ancestry groups.
  • Gene Constraint Analysis: Obtain gene-level scores like pLI and LOEUF to understand a gene's tolerance to loss-of-function mutations.
  • Coverage Assessment: Check read depth coverage for genomic regions to evaluate data quality.
  • Use Case: A researcher identifies a novel variant in a patient's exome data. They can use this Skill to query gnomAD to determine if the variant is common in any population, which is a crucial step in assessing its potential pathogenicity.

Quick Start

Use the gnomad-database skill to get the pLI and LOEUF scores for the gene BRCA1.

Frequently Asked Questions about gnomad-database

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

FAQPage Schema
How do I query gnomAD population variant frequencies using a GraphQL API?▼

To query gnomAD population variant frequencies, you can use a Skill that sends requests to the gnomAD v4 GraphQL API. It retrieves allele counts and frequencies across multiple ancestry groups by looking up specific variant IDs.

How do I retrieve gene constraint metrics like pLI and LOEUF for a specific gene?▼

Retrieving gene constraint metrics like pLI and LOEUF involves querying the gnomAD v4 GraphQL API with a specific gene symbol. This process returns scores indicating the gene's tolerance to loss-of-function mutations.

Can I check per-base read depth coverage for a genomic region in gnomAD?▼

Yes, you can check per-base read depth coverage for genomic regions in gnomAD. By querying the GraphQL API for targeted region-based analysis, you retrieve coverage data to evaluate sequencing data quality.

Do I need Python packages to retrieve gnomAD allele counts and frequencies?▼

Yes, retrieving gnomAD allele counts and frequencies requires the 'requests' Python package for API interaction. The workflow also relies on 'pandas' and 'matplotlib' for data handling and visualization.

What is the best way to assess variant rarity in exome data using population genetics databases?▼

The best way to assess variant rarity in exome data is querying gnomAD to retrieve population variant frequencies. This helps determine if a novel variant is common in any population, a crucial step in assessing pathogenicity.

Does gnomAD v4 GraphQL API support region-based queries for targeted variant analysis?▼

Yes, the gnomAD v4 GraphQL API supports region-based queries for targeted variant analysis. This allows users to retrieve population variant frequencies and coverage data for specific genomic intervals.

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