gnomad-variants

Query gnomAD allele frequencies and gene constraint scores via GraphQL API.

26|5|Updated Mar 8, 2026

Search Tags:#genomics #gnomad #variant annotation #allele frequency #gene constraint #population frequency

Ready to run

npx skills add https://github.com/ammawla/encode-toolkit --skill gnomad-variants

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gnomad-variants
Source: https://github.com/ammawla/encode-toolkit/tree/main/plugin/skills/gnomad-variants
Command: npx skills add https://github.com/ammawla/encode-toolkit --skill gnomad-variants

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires graphql, python-requests, and includes scripts (resource) components.

What problem does it solve?

This Skill enables querying gnomAD for detailed allele frequencies, population data, and gene constraint scores essential for interpreting ENCODE regulatory variants.

Core Features & Use Cases

Variant Frequency Analysis: Retrieve population-specific and global allele frequencies for genomic variants.
Gene Constraint Assessment: Access LOEUF, pLI, and other metrics to evaluate gene intolerance to loss-of-function mutations.
Use Case: When analyzing a regulatory variant within an ENCODE peak, check if it is rare in relevant populations and whether its target gene is highly constrained, prioritizing variants for functional validation.

Quick Start

Query gnomAD for the allele frequency of a specific variant to determine its rarity in different populations and evaluate gene constraint scores to assess potential pathogenicity.

Frequently Asked Questions about gnomad-variants

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

FAQPage Schema

How do I retrieve population allele frequencies for genomic variants?▼

You can retrieve population allele frequencies for genomic variants by querying gnomAD via a GraphQL API. This provides detailed global and population-specific prevalence data to support variant interpretation workflows.

What are gene constraint scores and when do I need them?▼

Gene constraint scores like LOEUF and pLI measure a gene's intolerance to loss-of-function mutations. You need them when prioritizing regulatory variants for functional validation to assess potential pathogenicity.

How do I check if a regulatory variant within an ENCODE peak is rare?▼

To check if a regulatory variant within an ENCODE peak is rare, query gnomAD for its allele frequency across different populations. This determines its prevalence and helps prioritize variants for downstream analysis.

Can I use python-requests to access gnomAD variant annotation data?▼

Yes, you can use python-requests to access gnomAD variant annotation data. The Skill utilizes python-requests alongside GraphQL to perform precise data retrieval for allele frequencies and gene constraint metrics.

Does this approach support integration into downstream variant prioritization processes?▼

Yes, this approach supports integration into downstream variant prioritization processes. It outputs allele frequency and gene constraint data that facilitate variant annotation and gene prioritization in genomic research workflows.

What is the best way to evaluate gene intolerance to loss-of-function mutations?▼

The best way to evaluate gene intolerance to loss-of-function mutations is accessing gnomAD gene constraint scores. Retrieving metrics like LOEUF and pLI allows you to assess the potential pathogenicity of target genes.