ClinVar SNVs annotated by VEP as Protein altering, after AVI positional overlap filtering.
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AVI six-model ensemble (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) | 0.9 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 sourceavi 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, 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)' |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
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7 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Original printed counts +50101/-101100 Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Positive count 50101 Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Source location Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Test count 151201 Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Description ClinVar SNVs annotated by VEP as Protein altering, after AVI positional overlap filtering. Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Relationship: used in 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) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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. |
| Name ClinVar 2025-06-15 SNVs, Protein altering (AlphaGenome Atlas test set) Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Fig. 2A panel header 'Protein altering (+50101/-101100)' (page 6) 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 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-subset-clinvar-snv-protein-altering