GPN-Star (M), mammalian, mutation-rate calibrated (AlphaGenome Atlas v1)
GPN-Star mammalian 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, 3' 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 (M), mammalian, 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, 3' UTR (AlphaGenome Atlas test set) | 0.18 AUPRC (ClinVar pathogenic vs benign SNVs, 3' 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-m on ClinVar 3' 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: '3’ UTR categories (0.50 vs. GPN-Star-M’s 0.18)' |
| Configuration: GPN-Star (M), mammalian, 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) | 0.26 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 (M) 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 (M) (AP=0.260)' (page 60) |
| Configuration: GPN-Star (M), mammalian, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: Rare complex-trait SNVs versus matched controls, AUPRC (AlphaGenome Atlas) Dataset: Rare variants associated with complex traits, UK Biobank and All of Us meta-analysis (AlphaGenome Atlas) | 0.67 AUPRC (rare complex-trait SNVs) unitless · higher Uncertainty: Not reported by the source: Fig. 2B 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-m on rare complex-trait SNVs (AlphaGenome Atlas Fig. 2B) ag-atlas-20261019-protocol-rare-complex-trait-snv-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. 2B: '(AUPRC 0.69 vs. GPN-Star-M’s 0.67)' |
| Configuration: GPN-Star (M), mammalian, 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) | 0.398 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 (M) 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 (M) (AUPRC = 0.398)' (page 57) |
| Configuration: GPN-Star (M), mammalian, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: TraitGym Mendelian non-coding variants, AUPRC after AVI filtering (AlphaGenome Atlas) Dataset subset: TraitGym Mendelian traits after AVI positional filtering (AlphaGenome Atlas) | 0.77 AUPRC (TraitGym Mendelian non-coding) unitless · higher Uncertainty: Not reported by the source: Fig. 2B 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-m on TraitGym Mendelian non-coding (AlphaGenome Atlas Fig. 2B) ag-atlas-20261019-protocol-traitgym-mendelian-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. 2B: 'AVI ranked second to GPN-Star-M (AUPRC 0.76 vs. 0.77)' |
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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-m
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- GPN-Star (M)
- 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-m on ClinVar 3' UTR SNVs (AlphaGenome Atlas Fig. 2A)
- system: GPN-Star (M) on the DNM1 minigene splicing screen (AlphaGenome Atlas fig. S9E)
- system: gpn-star-m on rare complex-trait SNVs (AlphaGenome Atlas Fig. 2B)
- system: GPN STAR (M) on pooled held-out SGE screens, snv (AlphaGenome Atlas fig. S7E)
- system: gpn-star-m on TraitGym Mendelian non-coding (AlphaGenome Atlas Fig. 2B)