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