---
license: odbl
task_categories:
  - tabular-classification
tags:
  - genomics
  - gnomad
  - allele-frequency
  - population-genetics
  - bioinformatics
  - sqlite
pretty_name: Allelix gnomAD Exome Frequencies
size_categories:
  - 10M<n<100M
---

# Allelix gnomAD Exome Frequency Cache

Pre-built SQLite cache of population allele frequencies from [gnomAD v4.1 exomes](https://gnomad.broadinstitute.org/) for use with [Allelix](https://github.com/dial481/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

```sql
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:

```bash
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](https://gnomad.broadinstitute.org/) (Broad Institute)
- **License:** [Open Data Commons Open Database License (ODbL) v1.0](https://opendatacommons.org/licenses/odbl/1-0/)
- **Citation:** See [gnomAD papers](https://gnomad.broadinstitute.org/publications)