| --- |
| license: apache-2.0 |
| tags: |
| - biology |
| - genomics |
| - dna |
| - variant-effect-prediction |
| --- |
| |
| # gnomAD v4.1 Variants with Consequence Annotations |
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| This dataset contains SNVs from gnomAD v4.1 genomes joined with variant consequence annotations. |
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| Code: https://github.com/gonzalobenegas/gnomad |
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| ## Columns |
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| ### Coordinates |
| - `chrom`: Chromosome (1-22, X, Y) |
| - `pos`: Position (1-based) |
| - `ref`: Reference allele |
| - `alt`: Alternate allele |
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| ### gnomAD Allele Frequencies |
| - `AC`: Allele count |
| - `AN`: Allele number |
| - `AF`: Allele frequency |
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| ### Consequence Annotations |
| Columns from [hg38-variant-consequences](https://huggingface.co/datasets/songlab/hg38-variant-consequences). |
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| ## Processing |
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| - Only PASS variants are included |
| - Only biallelic SNVs are included |
| - Left join with consequences |
| - Sorted by (chrom, pos, ref, alt) |
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| ## Sources |
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| - [gnomAD v4.1](https://gnomad.broadinstitute.org/) |
| - [hg38-variant-consequences](https://huggingface.co/datasets/songlab/hg38-variant-consequences) |
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