File size: 2,903 Bytes
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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)
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