Applying AlphaGenome Variant Impact for SNV Prioritization

Abstract

AlphaGenome Atlas, released in September 2026, provides functional predictions for nearly all possible human single-nucleotide variants using the AlphaGenome Variant Impact (AVI) score. However, empirical thresholds relating AVI quantile rank (AVI_QUANTILE) to clinical variant classifications have not been established. We derived AVI_QUANTILE thresholds distinguishing ClinVar pathogenic, likely pathogenic, uncertain, conflicting, likely benign, and benign SNVs using receiver operating characteristic analyses. Pathogenic/likely pathogenic variants were strongly enriched at the upper end of the AVI_QUANTILE distribution, yielding a Youden-optimal ClinVar-derived cutoff of 0.9938. Optimal cutoffs were generally consistent across several major molecular consequence classes, although lower thresholds were observed for selected noncoding categories. Similarly, most well-powered gene-disease groups showed cutoffs close to the global threshold, with modest gene-specific variation. Among 24,989 variants of uncertain significance, 11,357 (45.45%) exceeded the global cutoff, identifying a substantial subset with AlphaGenome-predicted functional effects comparable to those observed among pathogenic/likely pathogenic variants and potentially warranting further evaluation. In a steroid-dependent asthma fine-mapping analysis, AVI_QUANTILE showed little correspondence with SuSiE posterior inclusion probabilities, indicating that AlphaGenome functional predictions capture information distinct from statistical fine-mapping.