Dataset

ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)

Curated non-coding variants: 721 high-confidence pathogenic or functionally disruptive variants and 7,228 common benign variants.

Evaluation results

14 evaluations · 14 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AVI six-model ensemble (AlphaGenome Atlas v1)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.936 AUPRC (AVI baseline row, ncVar column) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AVI Model (Baseline) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Baseline', row 'AVI Model', column 'ncVar'
Configuration: AVI ablation 'All except AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-3.82% AUPRC relative difference (ablation 'All except AlphaGenome' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI All except AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'All except AlphaGenome', column 'ncVar'
Configuration: AVI ablation 'AlphaGenome' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-17.6% AUPRC relative difference (ablation 'AlphaGenome' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaGenome (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaGenome', column 'ncVar'
Configuration: AVI ablation 'AlphaMissense' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.18% AUPRC relative difference (ablation 'AlphaMissense' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI AlphaMissense (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'AlphaMissense', column 'ncVar'
Configuration: AVI ablation 'Cactus' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-0.91% AUPRC relative difference (ablation 'Cactus' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Cactus (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Cactus', column 'ncVar'
Configuration: AVI ablation 'Consequence' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.1% AUPRC relative difference (ablation 'Consequence' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Consequence (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Consequence', column 'ncVar'
Configuration: AVI ablation 'Conservation' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-4.26% AUPRC relative difference (ablation 'Conservation' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Conservation (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Conservation', column 'ncVar'
Configuration: AVI ablation 'Indel Type' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-0.44% AUPRC relative difference (ablation 'Indel Type' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Indel Type (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Indel Type', column 'ncVar'
Configuration: AVI ablation 'PhastCons' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.04% AUPRC relative difference (ablation 'PhastCons' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI PhastCons (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'PhastCons', column 'ncVar'
Configuration: AVI ablation 'Protein' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.1% AUPRC relative difference (ablation 'Protein' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Protein (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Protein', column 'ncVar'
Configuration: AVI ablation 'Splicing Removed Only' (Retrained, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	-15% AUPRC relative difference (ablation 'Splicing Removed Only' (Retrained) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI Splicing Removed Only (Retrained) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Retrained', row 'Splicing Removed Only', column 'ncVar'
Configuration: AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.06% AUPRC relative difference (ablation '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')' (Features Set to Zero) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Features Set to Zero', row '+ No Indel Type (second occurrence, below 'No AlphaMissense Indel Features')', column 'ncVar'
Configuration: AVI ablation 'No AlphaMissense Indel Features' (Features Set to Zero, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0% AUPRC relative difference (ablation 'No AlphaMissense Indel Features' (Features Set to Zero) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI No AlphaMissense Indel Features (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Features Set to Zero', row 'No AlphaMissense Indel Features', column 'ncVar'
Configuration: AVI ablation '+ No Indel Type' (Features Set to Zero, AlphaGenome Atlas Table S2)	Protocol: AVI feature ablation, ncVar column, AUPRC (AlphaGenome Atlas Table S2) Dataset: ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas)	0.06% AUPRC relative difference (ablation '+ No Indel Type' (Features Set to Zero) relative to the AVI baseline row, ncVar column) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source AVI + No Indel Type (Features Set to Zero) on ncVar (AlphaGenome Atlas Table S2) ag-atlas-20261019-protocol-table-s2-ncvar Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Table S2 (page 70), section 'Features Set to Zero', row '+ No Indel Type', column 'ncVar'

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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Evidence

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Evidence table

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Negatives 7228 Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.negatives` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact
Population fig. S7A after AVI filtering: SNVs +577/-4490, indels +18/-133 Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact
Positives 721 Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.positives` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact
Source location Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact
Description Curated non-coding variants: 721 high-confidence pathogenic or functionally disruptive variants and 7,228 common benign variants. Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact
Name ncVarDB non-coding pathogenic and benign variants (as used in AlphaGenome Atlas) Context-only references	AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Original source ↗ Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) Retrieved: 2026-10-19T12:19:03Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `b32d1539005ca4ea31c3dcef49b834424b1d8b5da4ce6b9fc3e1f942d39fc453` 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. Inspected artifact

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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)

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Technical metadata and extraction receipts

Stable ID: ag-atlas-20261019-data-ncvardb

areas: dna-genomes
contexts: research
positives: 721
negatives: 7228
population: fig. S7A after AVI filtering: SNVs +577/-4490, indels +18/-133
source locator: Methods 'ncVarDB Benchmark' (page 29); fig. S7A panel header

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