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gnomad-database

Query gnomAD GraphQL API for genetic variant frequencies and constraint metrics.

1|Updated Mar 12, 2026
Search Tags:#bioinformatics#genetics#variant interpretation#gnomad#allele frequency#gene constraint
One-click install
npx skills add https://github.com/yf8578/clawomics --skill gnomad-database-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/gnomad-database
Command: npx skills add https://github.com/yf8578/clawomics --skill gnomad-database-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the Genome Aggregation Database (gnomAD), enabling users to query population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance metrics for genetic variants.

Core Features & Use Cases

  • Variant Frequency Lookup: Determine if a variant is rare or common across diverse populations.
  • Pathogenicity Interpretation: Use allele frequencies and constraint scores to assess the clinical significance of genetic variants, crucial for rare disease diagnosis and variant classification.
  • Gene Prioritization: Identify genes that are intolerant to loss-of-function variants, aiding in the discovery of disease-causing genes.
  • Use Case: Given a list of variants from a patient's exome sequencing, use this Skill to check their allele frequencies in gnomAD and retrieve constraint scores for associated genes to aid in variant interpretation.

Quick Start

Query gnomAD for variants in the gene 'BRCA1' using the 'gnomad_r4' dataset.

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 for genetic variant allele frequencies and gene constraint scores?▼

To query gnomAD for genetic variant frequencies and gene constraint scores, use this Skill to access the gnomAD GraphQL API and retrieve population allele frequencies, pLI, and LOEUF metrics by gene symbol or variant ID.

Can I retrieve loss-of-function intolerance metrics like LOEUF for specific genes from gnomAD?▼

Yes, you can retrieve loss-of-function intolerance metrics like LOEUF and pLI for specific genes from gnomAD by querying the GraphQL API with a gene symbol to support gene prioritization and pathogenicity interpretation.

What is the best way to check population-stratified allele frequencies for exome sequencing variants?▼

The best way to check population-stratified allele frequencies for exome sequencing variants is querying gnomAD by specific variant ID or gene symbol to retrieve detailed frequency data essential for clinical variant classification.

Does this gnomAD query tool support variant lookup by both gene symbol and specific variant ID?▼

Yes, this gnomAD query tool supports variant lookup by both gene symbol and specific variant ID, enabling you to retrieve variant consequence annotations and population allele frequencies across diverse populations.

How do I use allele frequency and constraint data for variant pathogenicity interpretation?▼

To use allele frequency and constraint data for variant pathogenicity interpretation, query gnomAD to assess if a variant is rare or common and evaluate associated gene loss-of-function intolerance scores for rare disease diagnosis.

What are the limitations of querying gnomAD population data for variant interpretation?▼

A limitation of querying gnomAD population data for variant interpretation is that it relies on the gnomAD GraphQL API, meaning data availability is constrained by the specific datasets queried, such as gnomad_r4, and current database coverage.

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