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Benefit Ledger · provisional · Biology

AlphaGenome Atlas maps predicted effects of all 9 billion human SNVs

On 8 September 2026 Google DeepMind released AlphaGenome Atlas, a free academic catalogue of predicted molecular effects for every possible single-letter change in the human genome, plus a single AlphaGenome Variant Impact score.

8 Sep 2026Tier 3 MajorMethodology 0.1

Current score

+1.29

10 base · Major (tier 3 of 5, 10 pts)
× 0.9000 attribution · Primary causal contribution
× 0.4000 evidence · External expert evaluation
× 0.5500 realization · Experimentally validated
× 0.6500 durability
Event-level product before credit split: 1.29

A genome-wide public variant-effect atlas is a major research resource (tier 3), distinct from the January 2026 AlphaGenome method paper. High model attribution (0.90). Evidence is a DeepMind preprint plus Nature reporting, not peer review (0.40). Realization is a live academic portal and one reported research use, not a diagnostic (0.55). Durable as a database that will be revised (0.65).

What happened

Eight months after the AlphaGenome Nature paper, DeepMind published a 1-petabyte precomputed map covering the three substitutions at every hg38 base (~9 billion SNVs) and more than 100 million observed short insertions and deletions. The Atlas adds an AlphaGenome Variant Impact (AVI) score that compresses AlphaGenome regulatory predictions with AlphaMissense and conservation features into one ranking number, and a no-code portal for non-commercial research. Nature reported that the AVI score separated known pathogenic from benign variants in ClinVar-style tests in a DeepMind preprint, and that Broad Institute researchers used Atlas predictions to prioritize a non-coding candidate in a severe epilepsy case. This is not a diagnostic device and not a second score for the January 2026 method paper; it is the public, genome-wide lookup resource built from that model. Realization is a research database, not clinical care.

Model attribution

AlphaGenome

Sequence model whose genome-wide in silico saturation mutagenesis produced the Atlas predictions; AVI also draws on AlphaMissense and conservation features.

The catalogue is precomputed AlphaGenome output. AVI uses AlphaMissense as a feature, but the scored event is the AlphaGenome Atlas resource.

Attribution 0.9000 · Credit share 100% · Google DeepMind

Claims

  • DeepMind released a public academic atlas of predicted effects for all ~9 billion possible human SNVs, with an AVI ranking score and a research portal.

    outcome · supported

  • AlphaGenome Atlas is an approved clinical diagnostic for pathogenicity.

    outcome · disputed

Sources

primary sources

independent sources

Secondary domains: Medicine & Health

Revision history

  • 14 Sep 2026 · 0.00 1.29

    Imported events under methodology 0.1.

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