AlphaGenome and the AlphaGenome Atlas

AlphaGenome is DeepMind's sequence-to-function model: 1 Mb of DNA in, predictions at modality-specific resolutions for eleven assay types across thousands of human and mouse tracks out. The AlphaGenome Atlas (released 2026-09-08) is that model run once over every possible single-nucleotide change in GRCh38, about 9 billion variants, stored with a single ranking number, the AlphaGenome Variant Impact (AVI) score, its genome-wide percentile, and an 18-way attribution of what drives it. Both are reached through one pip install alphagenome and one API key.

Research and theoretical modelling only. API outputs must not be used to train other models, and are not for diagnostic procedures or medical decisions. Permissive-use downloads have separate terms; check the artifact licence.

When to use which

Setup

uv pip install alphagenome                     # PyPI; tested on Python 3.12 and 3.13, alphagenome 0.9.0
export ALPHAGENOME_API_KEY="..."               # https://deepmind.google.com/science/alphagenome
cd skills/alphagenome/scripts
python atlas_query.py scorers                  # proves key + network in one call

Shell examples quote variant strings because > otherwise redirects output. Network examples below are illustrative and were checked against SDK 0.9.0 contracts, without authenticated prediction/Atlas calls during this review.

Never put the key on a command line or in a file you commit; the scripts only read it from the environment. Authentication failures may surface as ValueError or PermissionError, depending on the gRPC status returned by the service.

The coordinate contract

• A variant is 1-based chr:pos:ref>alt (chr22:36201698:A>C). gnomAD (22-36201698-A-C), GTEx (chr22_36201698_A_C_b38), and Open Targets spellings are autodetected by the scripts. In the SDK, pass the matching variant_format=genome.VariantFormat.GNOMAD (or GTEX, OPEN_TARGETS, OPEN_TARGETS_BIGQUERY); from_str defaults to chr:pos:ref>alt.
• An interval on the command line is 1-based closed chr:start-end; the SDK's genome.Interval is 0-based half-open. The scripts convert.
• Human is GRCh38 only. The Atlas key is chr:pos:alt; REF is implied by the reference. Swapping REF/ALT can cause a miss; a wrong REF or build can misidentify a record. The scripts reject a returned variant that differs from the request, but cannot validate the build. Check REF against GRCh38 FASTA.
• rsIDs are not accepted by the API or the portal. Resolve them to coordinates.
• Use the chr prefix; MT becomes chrM.

Atlas workflow

1. Rank with AVI

python atlas_query.py avi --variant "chr22:36201698:A>C" "chr9:128225994:G>A"
python atlas_query.py avi --input candidates.vcf --min-phred 20 -o avi.tsv
python atlas_query.py avi --interval chr11:5225727-5226575 --top-k 25 -o hbb_window.tsv
python atlas_query.py avi --input credible_set.tsv --with-tracks -o avi_tracks.tsv

Output, one row per variant:

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