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

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 ( detailed in our paper ) 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.

Mapping rare variants associated with protein levels and complex traits. Moving beyond individual rare disease research, AlphaGenome Atlas can help uncover the genetic architecture of common traits in the general population. Identifying which rare, non-coding variants are associated with a specific trait or disease is notoriously difficult because the sheer volume of harmless genetic changes creates a statistical 'background noise'.

AlphaGenome Atlas is available today through an intuitive website portal, our AlphaGenome API, and as a skill in Google Antigravity .

Together, these resources support researchers for a wide range of genetic research tasks, from rapid variant ranking to deep dives into variant functions.

We wish to thank our teammates and collaborators for their technical support, feedback, including Kathryn Tunyasuvunakool, Alexander Karollus, Risha Patel, Francesca Pietra, Alisha Eastep, Doga Fadillioglu, Charlie Taylor, Raphael Aboyeji, Uchechi Okereke, Gemma Gibbs, Olufemi Duduyemi, Juan Mateos-Garcia, Mariana Felix, Sahar Abdulrahman, Antonia Mould, Rachael Tremlett, Chang Yun, Salil Deshpande, Anshul Kundaje, Samantha Bryen, Greg Findlay, Phoebe Dace, Kinga Bujakowska, Emma Sherrill, Aubrie Soucy Verran, Boxun Zhao, Tim Yu, Francesca Pietra, Brendah Namugamba, Cassie Gray, Daniel MacArthur, Lingyi Wang, Marc Mansour, Mohamad Hajjari, Mounica Vallurupalli, Philip Montgomery, Phoebe Dace, Roisin Sullivan, Sam Bryen, Teresa Niccoli,

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.