AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome

AlphaGenome Atlas: Molecular predictions for 9 Billion human DNA variants — Google DeepMind Skip to main content

September 8, 2026 Science AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome AlphaGenome Atlas team

Share

How predicting the molecular impact of every possible single-letter DNA variant in the human genome will help accelerate our understanding of biology. Today, we are introducing 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 is the most comprehensive catalogue of how genetic mutations affect molecular biology, and it is available for academic research through an intuitive and free-to-use website portal . DNA is the language of life. Mastering it is a grand challenge that could transform our ability to understand biology and treat disease. But progress has been limited by a fundamental problem: interpreting how genetic variations impact biology at a molecular level. With roughly 9 billion possible single-letter mutations in the human genome, testing each one in the lab is practically impossible. Google DeepMind has already made progress on this challenge with AlphaGenome, an artificial intelligence (AI) model that can predict how genetic variants impact biological processes. AlphaGenome is helpful for analyzing specific variants and has found widespread use in research, but we wanted to show researchers a big-picture view of variants across the entire genome. By precomputing AlphaGenome’s predictions at scale, we have created an easily accessible resource that vastly expands the model's reach. Just as an atlas is a collection of maps, linking together features of the land like altitude and location, AlphaGenome Atlas charts the molecular effects of DNA variants across the genome. To help scientists quickly find the most impactful genetic changes, we are also releasing the AlphaGenome Variant Impact (AVI) score. The AVI combines the strengths of AlphaGenome and AlphaMissense — our model for predicting the impact of protein-altering DNA variants — condensing both models’ predictions into a single number. Now, researchers can rapidly rank variants and interpret their molecular effects at the same time. Our trusted external collaborators have already used AlphaGenome Atlas to identify and experimentally verify key variants in unsolved rare disease research and find rare variants associated with common traits. AlphaGenome Atlas is available today through an intuitive website portal, our AlphaGenome API, and as a skill in Google Antigravity . AlphaGenome Atlas

AlphaGenome Atlas is a massive 1-petabyte dataset, more than 30 times larger than the AlphaFold Database. When we expanded the AlphaFold Database in 2022, we grew the 3D structure information available from around 190K experimental structures to more than 200M structure predictions — covering nearly all catalogued proteins known to science. The database provided a portal that researchers with no coding experience could use, providing intuitive visualizations and making it easier to do large-scale protein structure analysis. It quickly became a crucial resource that drove discoveries across the life sciences and continues to accelerate researchers’ important work in countless fields. In building AlphaGenome Atlas, we also aspire to make predictions more accessible and give scientists an intuitive way to explore a vast dataset. AlphaGenome Atlas provides several powerful, interconnected resources, allowing researchers to link variants directly to the functional DNA sequences they disrupt. Molecular effect predictions Atlas 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. This serves as the starting point for further resources. AVI score A single number describing the impact for each genetic variant. AVI feature attributions Each AVI score is also linked to distinct biological features driving it, such as the 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.

Together, these resources support researchers for a wide range of genetic research tasks, from rapid variant ranking to deep dives into variant functions. Extensive community collaboration guided the design of AlphaGenome Atlas. 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 orchestrates gene activity and houses most trait-associated variants. Our testing shows that the AVI score provides best-in-class performance across many variant pathogenicity and rare disease benchmarks. To help interpret these scores, we also calculated AVI feature attributions that highlight which molecular processes — like RNA splicing or gene expression — are predicted to be most disrupted by each variant.

Your browser does not support the video tag. Your browser does not support the video tag.

Overview of the AlphaGenome Atlas. (1) Precomputed effects are generated genome-wide for over 9 billion single-nucleotide variants. (2) From this, an allelic-resolution AlphaGenome Variant Impact (AVI) score is derived for each variant. To facilitate variant interpretation, AlphaGenome Atlas then decomposes the AVI score into additive feature contributions across interpretable categories such as chromatin accessibility, splicing, and conservation. (3) The precomputed variant effects, AVI score and the AVI feature attributions are linked, together with a compendium of genome-wide de novo motifs, which enables high-resolution mechanistic insights into variant function.

Real-world impact: From rare diseases to population genetics and molecular biology AlphaGenome Atlas provides a high-resolution, global view of the genome. These large-scale predictions become most useful when applied to targeted research questions. By translating this data into actionable biological insights, our academic partners are already uncovering links between genetic variation and disease. Understanding unsolved rare diseases. A major hurdle in...