GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1)
GPN-Star vertebrate model scoring all GRCh38 SNVs with the authors' code, calibrated with mutation rate; no indel scores.
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
5 evaluations · 5 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (ClinVar pathogenic vs benign SNVs, 5' UTR) (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.
All 5 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas) Dataset subset: ClinVar 2025-06-15 SNVs, Intronic (AlphaGenome Atlas test set) | 0.44 AUPRC (ClinVar pathogenic vs benign SNVs, Intronic) unitless · higher Uncertainty: Not reported by the source: Fig. 2A draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcegpn-star-v on ClinVar Intronic SNVs (AlphaGenome Atlas Fig. 2A) ag-atlas-20261019-protocol-clinvar-snv-by-consequence-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2A: 'intronic (AUPRC 0.76 vs. GPN-Star-V’s 0.44)' |
| Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas) Dataset subset: ClinVar 2025-06-15 SNVs, Protein altering (AlphaGenome Atlas test set) | 0.86 AUPRC (ClinVar pathogenic vs benign SNVs, Protein altering) unitless · higher Uncertainty: Not reported by the source: Fig. 2A draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcegpn-star-v on ClinVar Protein altering SNVs (AlphaGenome Atlas Fig. 2A) ag-atlas-20261019-protocol-clinvar-snv-by-consequence-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2A: 'protein-altering variants (0.90 vs. GPN-Star-V’s 0.86)' |
| Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas) Dataset subset: ClinVar 2025-06-15 SNVs, 5' UTR (AlphaGenome Atlas test set) | 0.27 AUPRC (ClinVar pathogenic vs benign SNVs, 5' UTR) unitless · higher Uncertainty: Not reported by the source: Fig. 2A draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcegpn-star-v on ClinVar 5' UTR SNVs (AlphaGenome Atlas Fig. 2A) ag-atlas-20261019-protocol-clinvar-snv-by-consequence-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2A: 'GPN-Star-V outperformed AVI on 5’UTR ClinVar SNVs (0.27 vs. 0.26)' |
| Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: DNM1 minigene screen, active versus inactive variants, average precision (AlphaGenome Atlas) Dataset: DNM1 intron saturation mutagenesis minigene splicing screen (AlphaGenome Atlas Data S1) | 0.348 Average precision (DNM1 minigene screen, active vs inactive variants) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN-Star (V) on the DNM1 minigene splicing screen (AlphaGenome Atlas fig. S9E) ag-atlas-20261019-protocol-dnm1-active-variant-ap Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S9E legend entry 'GPN-Star (V) (AP=0.348)' (page 60) |
| Configuration: GPN-Star (V), vertebrate, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: SGE held-out screens pooled, functionally abnormal versus normal SNVs, AUPRC (AlphaGenome Atlas) Dataset: Saturation genome editing screens of 13 genes from 14 studies (AlphaGenome Atlas) | 0.425 AUPRC (pooled held-out SGE screens, functionally abnormal vs normal, SNVs only) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPN STAR (V) on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E) ag-atlas-20261019-protocol-sge-pooled-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · fig. S7E (left) legend entry 'GPN STAR (V) (AUPRC = 0.425)' (page 57) |
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Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages)
Technical metadata and extraction receipts
Stable ID: ag-atlas-20261019-config-gpn-star-v
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- GPN-Star (V)
- missing metadata
- checkpoint revision: reason: unreported
- source locator
- Methods 'Obtaining baseline scores' (pages 26 to 27)
Related records
- configuration of: GPN-Star
- system: gpn-star-v on ClinVar Intronic SNVs (AlphaGenome Atlas Fig. 2A)
- system: gpn-star-v on ClinVar Protein altering SNVs (AlphaGenome Atlas Fig. 2A)
- system: gpn-star-v on ClinVar 5' UTR SNVs (AlphaGenome Atlas Fig. 2A)
- system: GPN-Star (V) on the DNM1 minigene splicing screen (AlphaGenome Atlas fig. S9E)
- system: GPN STAR (V) on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E)