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.