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gnomad-database

Query gnomAD genetic variation data via its GraphQL API.

Updated Mar 15, 2026
Search Tags:#bioinformatics#genetics#variant interpretation#gnomad#gene constraint#population frequency
One-click install
npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill gnomad-database-sagunkayastha
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/gnomad-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill gnomad-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides access to the Genome Aggregation Database (gnomAD), enabling users to query vast amounts of human genetic variation data for research and clinical interpretation.

Core Features & Use Cases

  • Variant Frequency Lookup: Determine if a genetic variant is rare or common in various populations.
  • Pathogenicity Assessment: Use allele frequencies and constraint scores (pLI, LOEUF) to help interpret the clinical significance of variants.
  • Gene Constraint Analysis: Identify genes that are intolerant to loss-of-function or missense variants.
  • Use Case: A researcher investigating a rare disease can use this Skill to check the population frequency of a candidate variant and assess if its associated gene is known to be intolerant to loss-of-function mutations.

Quick Start

Use the gnomad-database skill to find variants in 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 allele frequencies for genetic variant interpretation?▼

To query gnomAD population allele frequencies, use this Skill to programmatically access the gnomAD GraphQL API, retrieving specific variant frequency data and variant consequences for clinical pathogenicity assessment.

What is gene constraint analysis and how does LOEUF help identify loss-of-function intolerant genes?▼

Gene constraint analysis identifies genes intolerant to loss-of-function mutations. This Skill queries gnomAD to retrieve constraint metrics like pLI and LOEUF scores, helping pinpoint genes highly sensitive to functional disruption.

Can I use Python pandas to analyze gnomAD variant pathogenicity data?▼

Yes, you can use Python pandas to structure and analyze gnomAD variant pathogenicity data. This Skill returns population frequency and constraint metrics that integrate smoothly into pandas DataFrames for research analysis.

How do I check if a rare disease candidate variant is common in specific populations?▼

You can check candidate variant rarity by querying gnomAD for population allele frequencies. This Skill enables researchers to retrieve granular population frequency data to determine if a variant is rare across different cohorts.

Does the gnomAD database GraphQL API support querying missense and loss-of-function constraint metrics?▼

Yes, the gnomAD GraphQL API supports querying missense and loss-of-function constraint metrics. This Skill programmatically retrieves these gene constraint metrics to assist in evaluating variant clinical significance.

What are the limitations of using population frequency data for rare disease genetics research?▼

Population frequency data provides baseline rarity context but does not establish pathogenicity alone. This Skill retrieves allele frequencies and constraint scores to support, but not replace, comprehensive clinical variant interpretation.

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