Agent skill · research science · delphine-l
gnomad-database
Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance via GraphQL API. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.
Why this skill is useful
Provides specific GraphQL queries and templates for accessing gnomAD data that the AI wouldn't generate on its own.
What it needs
Requires gnomad account access. About 3k tokens when loaded. Last updated 2026-05-14. 17 stars on the source repository.
What this skill does
gnomAD Database Overview gnomAD is the largest publicly available collection of human genetic variation. gnomAD v4 contains exome sequences from 730,947 individuals and genome sequences from 76,215 individuals across diverse ancestries. Key resources: Browser: https://gnomad.broadinstitute.org/ GraphQL API: https://gnomad.broadinstitute.org/api Downloads: https://gnomad.broadinstitute.org/downloads When to Use This Skill Variant frequency lookup: Checking if a variant is rare, common, or absent Pathogenicity assessment: Filtering benign common variants (ACMG BA1/BS1/PM2) Loss-of-function intolerance: pLI and LOEUF scores for gene constraint Population-stratified frequencies: Comparing allele frequencies across ancestries Constraint analysis: Identifying genes depleted of missense or LoF variation Supporting Files graphqlqueries.md - Complete GraphQL query templates, population IDs, LoF annotation fields, in silico predictor IDs, Python helper with retry logic variantinterpretation.md - ACMG/AMP criteria thresholds, LoF assessment (LOFTEE), homozygous observations, in silico predictor score ranges, ancestry-specific considerations GraphQL API Endpoint: POST https://gnomad.broadinstitute.org/api Datasets: gnomadr4 (v4 exomes, GRCh38), gnomadr4genomes, gnomadr3 (GRCh38), gnomadr21 (GRCh37) Query Variants by Gene Query a Specific Variant Gene Constraint Scores Constraint score interpretation: Score Range Meaning ------- ------- --------- pLI 0-1 Probability of LoF intolerance; >0.9 = highly intolerant LOEUF 0-inf LoF observed/expected upper bound; <0.35 = constrained oelof 0-inf Observed/expected ratio for LoF variants misz -inf to inf Missense constraint z-score; >3.09 = constrained synz -inf to inf Synonymous z-score (control; should be near 0) LOEUF is preferred over pLI (less sensitive to sample size). …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills delphine-l/gnomad