The Atlas of Variant Effects (AVE) Alliance is a new organization aimed at the systematic, massively-scaled measurement of the biological effect of genetic variation in human, model organism and pathogen genomes to generate an atlas of thousands of variant effect maps for individual genes and associated regulatory elements. The atlas will be transformative, improving the fundamental understanding of biological mechanisms, empowering drug development and advancing clinical diagnosis and disease management. The Alliance will serve as a key forum to catalyse the assembly of this atlas by expanding the community of scientists who are developing and applying experimental and analytical technologies to generate variant effect maps, by supporting the community deploy resources wisely, and by establishing standards to ensure data are generated, managed and used responsibly and with maximum impact. This document articulates our vision to generate this atlas of variant effects. We summarise the potential impacts that would be enabled by the atlas. We describe the current state of the field and make a set of recommendations to address key challenges. Finally, we set out the values and organising principles of the AVE Alliance, and invite interested academic and industry researchers, clinicians, funders and others to join.

Also available at https://www.varianteffect.org/white-paper