08/09/2026
Variant impact prediction remains one of genomics’ greatest challenges. While coding variants have benefited from years of tool development, variants outside protein-coding regions have been much harder to assess.
AlphaGenome Variant Impact scores, developed by Google DeepMind, predict how likely variants across the whole human genome are to impact gene regulation.
The Ensembl Variant Effect Predictor (Ensembl VEP) now integrates AVI scores alongside its other evidence sources, available for the human reference genome GRCh38 via:
New Ensembl VEP: https://www.ensembl.org/tools/vep
Ensembl 116 archive: https://jun2026.archive.ensembl.org/
As a plugin for Ensembl VEP’s command-line package:
https://jun2026.archive.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
More on AlphaGenome Atlas and AlphaGenome Variant Impact scores: https://deepmind.google/blog/alphagenome-atlas-a-predictive-map-of-every-possible-dna-letter-change-in-the-human-genome/
