allelix/allelix-gnomad

Allelix gnomAD Exome Frequency Cache

Pre-built SQLite cache of population allele frequencies from gnomAD v4.1 exomes for use with Allelix.

What's in the file

exome_frequencies.sqlite.gz is a gzipped SQLite database containing the gnomad_frequencies table with all ~16M exome variants that carry an rsID in gnomAD v4.1.

Schema

CREATE TABLE gnomad_frequencies (
    chrom TEXT NOT NULL,
    pos INTEGER NOT NULL,
    ref TEXT NOT NULL,
    alt TEXT NOT NULL,
    rsid TEXT,
    af REAL,
    af_popmax REAL,
    popmax TEXT,
    af_afr REAL,
    af_amr REAL,
    af_asj REAL,
    af_eas REAL,
    af_fin REAL,
    af_nfe REAL,
    af_sas REAL,
    PRIMARY KEY (chrom, pos, ref, alt)
);

CREATE INDEX idx_gnomad_rsid ON gnomad_frequencies(rsid);

Columns

Column	Description
chrom	Chromosome (1-22, X, Y, no "chr" prefix)
pos	Genomic position (GRCh38)
ref	Reference allele
alt	Alternate allele
rsid	dbSNP rsID
af	Global allele frequency
af_popmax	Maximum allele frequency across populations
popmax	Population with the highest frequency
af_afr	African/African American frequency
af_amr	Admixed American/Latino frequency
af_asj	Ashkenazi Jewish frequency
af_eas	East Asian frequency
af_fin	Finnish frequency
af_nfe	Non-Finnish European frequency
af_sas	South Asian frequency

Multi-allelic sites

The composite primary key (chrom, pos, ref, alt) preserves multi-allelic sites. A single rsID may have multiple rows with different alternate alleles. For example, rs776646858 has 13 distinct ALT alleles in the exome dataset.

How Allelix uses this

Allelix downloads this file automatically during allelix db update. The annotator looks up variants by rsID and returns MAX(af) across alleles for a given rsID. Coordinate columns are indexed for future integration with AlphaMissense and CADD scores.

Building from source

The cache can be rebuilt from gnomAD exome VCFs using the build script included with Allelix:

python scripts/build_gnomad_cache.py --full --local-dir /path/to/gnomad/vcfs --output exome_frequencies.sqlite
gzip exome_frequencies.sqlite

Source and license

• Source: gnomAD v4.1 exomes (Broad Institute)
• License: Open Data Commons Open Database License (ODbL) v1.0
• Citation: See gnomAD papers