AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome
2026-09-08 · Google DeepMind
AlphaGenome Atlas: A Predictive Map of DNA Letter Changes
On September 8, 2026, the AlphaGenome Atlas team introduced AlphaGenome Atlas, a platform containing predictions for the effects of 9 billion single-nucleotide variants—every single-letter change possible—in the human genome. It serves as the most comprehensive catalogue of how genetic mutations affect molecular biology. The platform is available for academic research through a free-to-use website portal, the AlphaGenome API, and as a skill in Google Antigravity.
Background and Vision
DNA is the language of life, but interpreting how genetic variations impact biology at a molecular level has been a fundamental challenge. With roughly 9 billion possible single-letter mutations in the human genome, lab-testing each one is practically impossible. Google DeepMind previously developed AlphaGenome, an AI model that predicts how genetic variants impact biological processes. However, to provide researchers with a big-picture view across the entire genome, the team precomputed AlphaGenome’s predictions at scale to create this easily accessible resource.
Core Resources of AlphaGenome Atlas
AlphaGenome Atlas is a massive 1-petabyte dataset, more than 30 times larger than the AlphaFold Database. It provides several powerful, interconnected resources that allow researchers to link variants directly to the functional DNA sequences they disrupt:
- Molecular effect predictions: Contains thousands of molecular effect predictions for each variant across multiple important aspects of gene regulation, spanning hundreds of human and mouse cell types and tissues.
- AVI score: The AlphaGenome Variant Impact (AVI) score combines the strengths of AlphaGenome and AlphaMissense (a model for predicting protein-altering DNA variants), condensing both models’ predictions into a single number.
- AVI feature attributions: Each AVI score is linked to distinct biological features driving it, such as aspects of gene regulation predicted by AlphaGenome or the protein impact score from AlphaMissense.
- DNA sequence motifs: A comprehensive collection of over 2,500 recurrent DNA sequences—the "words" of the genome—and their locations.
Advantages and Applications of the AVI Score
The AVI score helps researchers rapidly score and rank variants based on their potential impact. Crucially, it works for both coding regions (the 2% of the genome that codes for proteins) and non-coding regions (the remaining 98%), which orchestrate gene activity and house most trait-associated variants.
Testing shows that the AVI score provides best-in-class performance across many variant pathogenicity and rare disease benchmarks. To help interpret these scores, the platform also calculates AVI feature attributions that highlight which molecular processes—like RNA splicing or gene expression—are predicted to be most disrupted by each variant.
Real-World Impact
Guided by extensive community collaboration, AlphaGenome Atlas supports a wide range of genetic research tasks, from rapid variant ranking to deep dives into variant functions. Trusted external collaborators have already utilized the platform to identify and experimentally verify key variants in unsolved rare disease research, as well as to find rare variants associated with common traits. The platform provides a high-resolution, global resource for advancing our understanding of biology and treating disease.