Developer-reported comparison transcribed from the pinned source; not reproduced.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
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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, 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)' |
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ClinVar pathogenic versus benign SNVs by VEP consequence, AUPRC (AlphaGenome Atlas)
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation None for comparators; AVI trained on gnomAD frequency labels, not ClinVar Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: aggregation One AUPRC per consequence class Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: budget Not reported Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: dataset version ClinVar 2025-06-15 Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: inputs Precomputed or model-derived score per variant Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: metric implementation AUPRC Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: population ClinVar Protein altering SNVs, +50101/-101100 (positives/negatives) Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: protocol id ag-atlas-20261019-protocol-clinvar-snv-by-consequence-auprc Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Comparison: split AVI positional test filter Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Origin author_reported Context-only references | 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; Fig. 2A panel 'Protein altering' Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: ag-atlas-20261019-eval-clinvar-snv-protein-altering-gpn-star-v