| --- |
| 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) |
|
|
