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AlphaGenome splice site, raw, maximum (Lu et al. 2025)

AlphaGenome variant score taken as the maximum raw splice site score.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaGenome splice site, raw, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.706 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice site (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice site (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice site (raw)', bar label

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Original source · bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages)

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Technical metadata and extraction receipts

Stable ID: lu-hetero-20261019-config-alphagenome-splice-site-raw

areas: dna-genomes
contexts: clinical_research
method types: foundation_model
reported name: Splice site (raw)
parameters: Official AlphaGenome API (deepmind.google.com/science/alphagenome), 1 Mbp input context centred on the variant, organism human, all output modalities enabled (5,930 human genomic annotations across 11 modalities). Splice site output only, raw scores, maximum over outputs.
access reuse: Official AlphaGenome API
source locator: Methods 'AlphaGenome' (pages 16 to 17); Supplementary Figure S2
missing metadata: model version: reason: unreported; note: API model version and query date not printed.

Related records

configuration of: AlphaGenome
system: AlphaGenome Splice site (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2)

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