gnomad-database
Access the Genome Aggregation Database via GraphQL API to retrieve population allele frequencies, loss-of-function intolerance metrics, and variant annotations across diverse ancestries. Essential for filtering benign variants and identifying genes depleted of protein-truncating variation in rare disease genetics and pathogenicity assessment.
gnomad-database queries population allele frequencies and constraint scores to assess variant pathogenicity in genetic analysis.
AI-generated summary based on this skill's SKILL.md
Decision gist · record as of 2026-06-08
gnomad-database queries population allele frequencies and constraint scores to assess variant pathogenicity in genetic analysis. Access the Genome Aggregation Database via GraphQL API to retrieve population allele frequencies, loss-of-function intolerance metrics, and variant annotations across diverse ancestries. Essential for filtering benign variants and identifying genes depleted of protein-truncating variation in rare disease genetics and pathogenicity assessment.
Use it when
- gnomad-database surfaces pLI (probability of loss-of-function intolerance) and LOEUF (loss-of-function observed/expected upper bound.
- Yes, gnomad-database enables filtering rare variants by ancestry-specific allele frequencies across diverse populations.
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Install
beita6969/ScienceClaw/gnomad-database · repository language: TypeScript
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Frequently asked questions
AI-generated answers based on this skill's SKILL.md and metadata
How do I check allele frequency in gnomAD for variant interpretation?
gnomad-database provides GraphQL API access to query allele frequencies across diverse populations. You can retrieve variant frequencies stratified by ancestry, apply ACMG criteria (BA1/BS1/PM2) thresholds, and assess pathogenicity. The database includes exome and genome data from gnomAD v4, enabling you to filter rare variants and determine if a variant meets benign classification criteria based on population frequency cutoffs.
What are pLI and LOEUF constraint metrics in gnomad-database?
gnomad-database surfaces pLI (probability of loss-of-function intolerance) and LOEUF (loss-of-function observed/expected upper bound fraction) scores to identify genes depleted of protein-truncating variation. These metrics help prioritize candidate genes in rare disease research by highlighting which genes are intolerant to loss-of-function mutations, distinguishing them from genes where such variants are tolerated in the population.
Can gnomad-database filter variants by ancestry-specific frequencies?
Yes, gnomad-database enables filtering rare variants by ancestry-specific allele frequencies across diverse populations. You can query population-stratified data to assess whether a variant is truly rare in your population of interest, avoiding false pathogenicity calls driven by enrichment in underrepresented ancestries. This ancestry-aware filtering is critical for accurate variant interpretation in diverse cohorts.
How does gnomad-database support ACMG pathogenicity criteria?
gnomad-database supplies the population frequency data needed to apply ACMG criteria BA1 (benign standalone), BS1 (benign strong), and PM2 (pathogenic moderate). By querying gnomAD allele frequencies via GraphQL API, you can determine whether variants exceed established thresholds and automatically classify them according to ACMG guidelines for clinical variant interpretation.
What data types does gnomad-database include beyond SNVs?
gnomad-database covers exome and genome variants from gnomAD v4, including structural variants. Beyond single nucleotide variants, you can access indels, copy number variations, and other structural rearrangements annotated with population frequencies and constraint metrics, providing comprehensive coverage for rare disease genetics research and variant prioritization workflows.
How can I query gnomad-database programmatically?
gnomad-database exposes a GraphQL API for programmatic access. You can construct queries to retrieve variant frequencies, gene constraint scores, and population-stratified annotations. The API supports Python and other languages, allowing you to integrate gnomAD data into automated pipelines for batch variant interpretation, candidate gene prioritization, and pathogenicity assessment workflows.
SKILL.md
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gnomAD Database
Overview
The Genome Aggregation Database (gnomAD) is the largest publicly available collection of human genetic variation, aggregated from large-scale sequencing projects. gnomAD v4 contains exome sequences from 730,947 individuals and genome sequences from 76,215 individuals across diverse ancestries. It provides population allele frequencies, variant consequence annotations, and gene-level constraint metrics that are essential for interpreting the clinical significance of genetic variants.
Key resources: - gnomAD browser: https://gnomad.broadinstitute.org/ - GraphQL API: https://gnomad.broadinstitute.org/api - Data downloads: https://gnomad.broadinstitute.org/downloads - Documentation: https://gnomad.broadinstitute.org/help
When to Use This Skill
Use gnomAD when:
-
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skills/gnomad-database/SKILL.md
skills/gnomad-database/references/graphql_queries.md
skills/gnomad-database/references/variant_interpretation.md
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Related skills
Gnomad accesses the Genome Aggregation Database to retrieve allele frequencies, constraint metrics, and loss-of-function annotations across diverse populations. Use it to assess variant rarity, filter benign variants by ACMG criteria, and identify genes intolerant of functional disruption through pLI and LOEUF scores.
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