rewirebio.iobenchmarks
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Pipeline

AlphaGenome Variant Impact (AVI)

Scores the impact of SNVs and indels with a small neural network over 18 features: ten AlphaGenome modality scores, AlphaMissense, two conservation scores, three VEP loss-of-function indicators and two indel-type indicators, trained to separate rare from common gnomAD variants.

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Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Stable ID: ag-atlas-20261019-pipeline-avi

areas
dna-genomes
contexts
research
method types
supervised_machine_learning
configuration type
pipeline
reported name
AVI (AlphaGenome Variant Impact)
version
AlphaGenome Atlas medRxiv v1
parameters
Inputs: AlphaGenome scores (10 features: ATAC, contact maps, DNase, ChIP-TF, ChIP-histone, CAGE, PRO-cap, RNA-seq, polyadenylation and one merged splicing score, each the maximum absolute value over tracks and genes, active-allele scorers excluded); AlphaMissense (1); Zoonomia Cactus 241-way phyloP (1); PhastCons 470-way (1); VEP protein termination, stop lost and start lost indicators (3); insertion and deletion indicators (2). Labels: gnomAD v4.1 genome FAF95_GRPMAX above versus below 0.1% (proxy neutral versus proxy impactful), trinucleotide-matched balanced sampling. Training chromosomes 1, 4, 7, 8, 10, 13 and 15. Raw logits converted to PHRED scores.
access
Precomputed AVI scores and feature attributions through an API and https://alphagenome.google/atlas
source locator
Results 'Whole genome in silico mutagenesis...' paragraph 2; Methods 'AlphaGenome Variant Impact Scores' (pages 20 to 26)
provenance note
Introduced in the AlphaGenome Atlas preprint (medRxiv v1). The checkpoint files are not published in the paper.
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