gnomad-database

# gnomAD Database ## Overview The Genome Aggregation Database (gnomAD) is a resource of aggregated exome and genome sequencing data from 730,000+ individuals. It provides population variant frequencies stratified by 9 ancestry groups, gene-level constraint scores (pLI, LOEUF), and read coverage information. Access is free via a GraphQL API at `https://gnomad.broadinstitute.org/api` — no authentication required, no official SDK. ## When to Use - Checking whether a candidate variant is rare enough to be clinically relevant (AF < 0.1% in all populations) - Retrieving allele frequencies stratified by ancestry group (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID) for a variant - Identifying all rare loss-of-function variants in a gene for burden testing or candidate prioritization - Getting gene constraint metrics (pLI, LOEUF) to assess tolerance to loss-of-function variants - Checking read depth coverage for a region to evaluate if low variant frequency reflects low sequencing coverage - Filtering a VCF by population frequency — query gnomAD AF to discard common variants before clinical interpretation - For clinical pathogenicity classifications use `clinvar-database`; gnomAD provides frequency evidence but does not classify pathogenicity - For GWAS associations at the study level use `gwas-database`; gnomAD is for population frequency lookups ## Prerequisites - **Python packages**: `requests`, `pandas`, `matplotlib` - **Data requirements**: gene symbols (e.g., `BRCA1`), variant I...