gnomad-variantslisted

# Query gnomAD for Population Variant Data ## When to Use - User wants to check population allele frequencies for variants in ENCODE regulatory regions - User asks about "gnomAD", "allele frequency", "population genetics", "gene constraint", or "variant frequency" - User needs to filter regulatory variants by rarity (common vs rare) using population data - User wants to assess gene constraint (pLI, LOEUF) for targets identified from ENCODE ChIP-seq - Example queries: "check gnomAD frequency for variants in my peaks", "is this regulatory variant rare?", "what's the constraint score for CTCF?" Annotate ENCODE-identified regulatory variants with population allele frequencies and gene constraint scores from the Genome Aggregation Database. ## Scientific Rationale **The question**: "How common is this variant in the population, and how constrained is the gene it regulates?" ENCODE identifies regulatory elements and the variants within them, but does not provide population frequency data. gnomAD (v4.1: 807,162 individuals, 730,947 exomes + 76,215 genomes) fills this gap — enabling researchers to distinguish common regulatory variants (likely benign or with modest effect) from rare variants (potentially pathogenic or high-impact). ### Why gnomAD + ENCODE Together | ENCODE Provides | gnomAD Provides | Combined Insight | |----------------|----------------|------------------| | Variant overlaps cCRE (dELS) | AF = 0.0001 (rare) | Rare variant disrupting an enhancer → high priori