Configuration
AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)
AlphaGenome variant score taken as the maximum quantile (percentile) over all outputs after converting each output to quantiles.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
15 evaluations · 15 results. Different protocols are not a single leaderboard.
Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)
Sorted by AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All outputs (quantile)') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All outputs (quantile)') | AUROC (ClinVar pathogenic vs benign SNVs, 3' UTR) | AUROC (ClinVar pathogenic vs benign SNVs, 5' UTR) | AUROC (ClinVar pathogenic vs benign SNVs, All variants) | AUROC (ClinVar pathogenic vs benign SNVs, Intron (Non-splice)) | AUROC (ClinVar pathogenic vs benign SNVs, Missense & 3'UTR) | AUROC (ClinVar pathogenic vs benign SNVs, Missense & Intron (Non-splice)) | AUROC (ClinVar pathogenic vs benign SNVs, Missense) | AUROC (ClinVar pathogenic vs benign SNVs, Noncoding) | AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) | AUROC (ClinVar pathogenic vs benign SNVs, Splice) | AUROC (ClinVar pathogenic vs benign SNVs, Start loss) | AUROC (ClinVar pathogenic vs benign SNVs, Stop gain) | AUROC (ClinVar pathogenic vs benign SNVs, Stop loss) | AUROC (ClinVar pathogenic vs benign SNVs, Synonymous) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2) | 0.614 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: All variants (Figure 1) | Not reported | Not reported | Not reported | 0.31 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Intron (Non-splice) (Figure 1) | Not reported | Not reported | Not reported | Not reported | 0.96 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.56 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense & Intron (Non-splice) (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.583 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Missense & 3'UTR (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | 0.508 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Noncoding (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.991 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: RNA gene (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.851 | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Splice (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.592 | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Start loss (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.523 | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Stop gain (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.389 | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Stop loss (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.362 | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: Synonymous (Figure 1) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.919 |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: 3' UTR (Figure 1) | Not reported | 0.789 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)Evaluation | Lu et al. 2025 ClinVar benchmark: 5' UTR (Figure 1) | Not reported | Not reported | 0.58 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 15 result rows with coverage, uncertainty and sources
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Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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How it works, versions and access
Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this configuration. Consult the linked sources and evaluation records below.
Evidence
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Evidence table
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- 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)
Technical metadata and extraction receipts
Stable ID: lu-hetero-20261019-config-alphagenome-all-outputs-quantile
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- foundation_model
- reported name
- AlphaGenome
- 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). Recommended implementation: each output converted to quantiles; the variant gets the maximum percentile observed across all outputs, relevant or not to the variant type. Used for every Figure 1 panel.
- 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
- subject: AlphaGenome scoring setup in Lu et al. 2025
- system: AlphaGenome on ClinVar All variants SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Intron (Non-splice) SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Missense SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Missense & Intron (Non-splice) SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Missense & 3'UTR SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Noncoding SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Splice SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome All outputs (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2)
- system: AlphaGenome on ClinVar Start loss SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Stop gain SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Stop loss SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar Synonymous SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar 3' UTR SNVs (Lu et al. 2025 Figure 1)
- system: AlphaGenome on ClinVar 5' UTR SNVs (Lu et al. 2025 Figure 1)