gnomad-database

Retrieve gnomAD allele frequencies and constraint metrics via GraphQL.

783|65|Updated Feb 27, 2026
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gnomad-database-leonchaox
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: gnomad-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/gnomad-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gnomad-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

It solves the problem of interpreting genetic variants by retrieving population allele frequencies, constraint metrics, and loss-of-function intolerance evidence from gnomAD.

Core Features & Use Cases

  • Variant frequency lookup (by gene or variant ID): Determine whether a variant is rare, common, or absent in gnomAD and retrieve allele counts across datasets.
  • Constraint and LoF intolerance (pLI, LOEUF): Prioritize candidate genes for rare disease research using gene-level tolerance to loss-of-function variants.
  • Population-stratified frequencies: Compare allele frequencies across ancestries to support ancestry-aware interpretation and study design.
  • Clinical interpretation workflows: Support evidence assignment aligned with common ACMG/AMP reasoning for benign vs pathogenic likelihood.

Quick Start

Use the gnomad-database skill to query gnomAD for a specific gene’s variants and extract key fields like allele frequency and LoF annotation.

Frequently Asked Questions about gnomad-database

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

FAQPage Schema
How do I retrieve gnomAD population allele frequencies for a specific genetic variant?

To retrieve gnomAD population allele frequencies, query the gnomAD GraphQL API endpoint with a selected dataset like gnomad_r4 to extract allele frequency, allele count, and allele number fields for your specific variant ID.

What does gene constraint and LoF intolerance mean in population genetics?

Gene constraint and LoF intolerance indicate whether a gene is depleted of loss-of-function variants in the gnomAD population. Metrics like pLI and LOEUF help prioritize candidate genes for rare disease research by measuring intolerance to such variation.

Can I compare ancestry-aware allele frequencies across different populations using gnomAD?

Yes, you can compare ancestry-aware allele frequencies by querying the gnomAD GraphQL API to retrieve population-stratified frequency data, supporting ancestry-aware interpretation and study design for human genetic variants.

How do I use gnomAD constraint metrics for clinical variant interpretation?

Use gnomAD constraint metrics like pLI, LOEUF, and oe_lof/oe_mis to support clinical interpretation workflows. These metrics help assign evidence aligned with ACMG/AMP reasoning for benign versus pathogenic likelihood in rare disease genomics.

Does this approach work with the gnomAD GraphQL API for gene-level variant retrieval?

Yes, querying the gnomAD GraphQL API supports gene-level variant retrieval by extracting consequence and LoF fields like lof and lof_flags alongside frequency data, enabling comprehensive variant interpretation across specified datasets.