gnomad-database

Query gnomAD GraphQL API for allele frequencies and variant annotations.

Updated Mar 10, 2026

Search Tags:#genetics #variant interpretation #gnomad #allele frequency #population genetics #gene constraint

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill gnomad-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/gnomad-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill gnomad-database-yezez9

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 human genetic variation data for allele frequencies, variant constraint scores, and pathogenicity interpretation.

Core Features & Use Cases

Variant Frequency Lookup: Determine if a genetic variant is rare or common in human populations.
Pathogenicity Assessment: Use allele frequencies and constraint metrics (pLI, LOEUF) to help interpret the clinical significance of variants.
Population Genetics: Analyze allele frequencies across diverse ancestries.
Use Case: A geneticist needs to assess a novel variant found in a patient with a rare disease. They use this Skill to check its frequency in gnomAD and its impact on gene constraint to aid in diagnosis.

Quick Start

Use the gnomad-database skill to query for 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 for population allele frequencies?▼

Retrieve gnomAD allele frequencies by using this Skill to programmatically query the database via its GraphQL API. It provides population allele frequencies and consequence annotations for human genetic variants.

What is gnomAD gene constraint and how do I get pLI scores?▼

gnomAD gene constraint metrics like pLI and LOEUF measure a gene's intolerance to loss-of-function variation. You can retrieve these constraint scores by querying gene-level metrics through the provided GraphQL API.

Can I use Python to check gnomAD variant frequency for pathogenicity interpretation?▼

Yes, you can use Python to check gnomAD variant frequencies for pathogenicity interpretation. This Skill leverages the requests and pandas libraries to query the GraphQL API and structure the returned variation data.

Does this approach work for retrieving structural variant data from gnomAD?▼

Yes, this approach works for retrieving structural variant data from gnomAD. The Skill supports programmatic querying of the GraphQL API to access comprehensive human genetic variation, including structural variants.

What is the best way to access gnomAD population genetics data for rare disease research?▼

The best way to access gnomAD population genetics data for rare disease research is using a programmatic GraphQL API query. This facilitates retrieval of allele frequencies and constraint metrics to aid diagnosis.

Why do I need pandas to query human genetic variation data?▼

You need pandas to structure and analyze the human genetic variation data retrieved from the gnomAD GraphQL API. It handles the tabular formatting of population allele frequencies and gene constraint metrics.