Does this skill require a local copy of the gnomAD database?

No, it interacts directly with the official gnomAD GraphQL API, allowing you to fetch the most recent data without hosting large VCF files locally.

Can I use this for ACMG variant classification?

Yes, it provides the allele frequency data required for BA1 (Benign Stand-Alone), BS1 (Benign Supporting), and PM2 (Pathogenic Moderate) evidence codes.

How do I interpret the LOEUF score provided by this skill?

LOEUF (Loss-of-function observed/expected upper bound fraction) measures gene constraint; a score below 0.35 typically indicates a gene is highly intolerant to loss-of-function variation.

Which gnomAD versions does this skill support?

The skill supports gnomAD v4 (exomes and genomes), v3 (genomes), and v2.1.1 (exomes), covering both GRCh38 and GRCh37 reference genomes.

gnomAD Genomics & Variant Analysis

Name: gnomAD Genomics & Variant Analysis
Author: Yezez9

byYezez9

0•

Ciencia de Datos y ML

Queries the Genome Aggregation Database (gnomAD) for population allele frequencies, variant consequences, and gene constraint metrics.

This skill enables programmatic interaction with the Genome Aggregation Database (gnomAD), the world's largest collection of human genetic variation. It provides a structured interface for querying gnomAD's GraphQL API to retrieve critical data such as population-stratified allele frequencies, loss-of-function intolerance scores (pLI, LOEUF), and missense constraint Z-scores. Designed for bioinformaticians and clinical researchers, it streamlines the process of variant pathogenicity assessment, rare disease gene prioritization, and population genetics research across both GRCh37 and GRCh38 reference genomes.

Características Principales

01Retrieval of gene constraint metrics including pLI, LOEUF, and Z-scores

02Automated GraphQL API querying for gnomAD v2, v3, and v4 datasets

030 GitHub stars

04Integration workflows for ACMG/ClinVar variant classification criteria

05Detailed variant lookup including population-specific allele frequencies (AF/AC/AN)

06Structural variant (gnomAD-SV) overlap analysis by gene symbol

Casos de Uso

01Assessing the rarity and clinical significance of genetic variants for rare disease diagnosis

02Analyzing ancestry-specific allele frequencies for population genetics and GWAS follow-up

03Prioritizing candidate genes in exome/genome sequencing pipelines using constraint scores

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent gnomad-database

For use in Claude.ai and ChatGPT

Características Principales

01Retrieval of gene constraint metrics including pLI, LOEUF, and Z-scores

02Automated GraphQL API querying for gnomAD v2, v3, and v4 datasets

030 GitHub stars

04Integration workflows for ACMG/ClinVar variant classification criteria

05Detailed variant lookup including population-specific allele frequencies (AF/AC/AN)

06Structural variant (gnomAD-SV) overlap analysis by gene symbol

Casos de Uso

01Assessing the rarity and clinical significance of genetic variants for rare disease diagnosis

02Analyzing ancestry-specific allele frequencies for population genetics and GWAS follow-up

03Prioritizing candidate genes in exome/genome sequencing pipelines using constraint scores