Dataset subset

Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)

ClinVar canonical splice-site SNVs (within 1 to 2 nt of an exon boundary) scored by the AlphaGenome scorers compared in Supplementary Figure S2.

Evaluation results

9 evaluations · 9 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaGenome all outputs, quantile, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.614 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All outputs (quantile)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome All outputs (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'All outputs (quantile)', bar label
Configuration: AlphaGenome splice junction, quantile, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.6 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice junction (quantile)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice junction (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice junction (quantile)', bar label
Configuration: AlphaGenome splice junction, raw, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.669 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice junction (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice junction (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice junction (raw)', bar label
Configuration: AlphaGenome splice composite, quantile scores (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.614 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All splice outputs (quantile)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome All splice outputs (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'All splice outputs (quantile)', bar label
Configuration: AlphaGenome splice composite, raw scores (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.708 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'All splice outputs (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome All splice outputs (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'All splice outputs (raw)', bar label
Configuration: AlphaGenome splice site, quantile, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.683 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice site (quantile)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice site (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice site (quantile)', bar label
Configuration: AlphaGenome splice site, raw, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.706 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice site (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice site (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice site (raw)', bar label
Configuration: AlphaGenome splice site usage, quantile, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.699 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice site usage (quantile)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice site usage (quantile) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice site usage (quantile)', bar label
Configuration: AlphaGenome splice site usage, raw, maximum (Lu et al. 2025)	Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025) Dataset subset: Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2)	0.779 AUROC (ClinVar pathogenic vs benign canonical splice SNVs (N=11,047); AlphaGenome scorer 'Splice site usage (raw)') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaGenome Splice site usage (raw) on ClinVar splice variants (Lu et al. 2025 Supplementary Figure S2) lu-hetero-20261019-protocol-clinvar-variant-type-auroc Aggregation: Not reported Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Supplementary Figure S2 (page 21), row 'Splice site usage (raw)', bar label

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8 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
Limitations 1 values Figure 1 'Splice' has N=11,042; the five-variant difference is not explained, so the two splice AUROCs for the all-outputs scorer (0.592 and 0.614) are on different variant sets. Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Original printed counts N=11,047, %P=99.32% Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.original_printed_counts` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Source location Supplementary Figure S2 legend (page 21) Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Test count 11047 Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.test_count` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Description ClinVar canonical splice-site SNVs (within 1 to 2 nt of an exon boundary) scored by the AlphaGenome scorers compared in Supplementary Figure S2. Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Relationship: same data as lu-hetero-20261019-subset-splice Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `links:same_data_as:lu-hetero-20261019-subset-splice` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Relationship: used in lu-hetero-20261019-protocol-clinvar-variant-type-auroc Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `links:used_in:lu-hetero-20261019-protocol-clinvar-variant-type-auroc` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact
Name Lu et al. 2025 ClinVar benchmark: splice variants scored by AlphaGenome (Supplementary Figure S2) Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Supplementary Figure S2 legend (page 21) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) Retrieved: 2026-10-19T12:23:08Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `5b8e939257000811a6eaddd90d9de3e03bf1ac0e9015a38769df887ee01f9bf2` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF on each download: a second retrieval at 2026-10-19T12:31:50Z had the same length (1,100,277 bytes), SHA-256 1a1aa1135ad8aa59bdb949bf8df75262eb6feba51b47f49439dbb819c426fbdd, differed in 32 bytes (ModDate) and had an identical pdftotext -layout text layer. Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) · Original source · bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages)

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Technical metadata and extraction receipts

Stable ID: lu-hetero-20261019-subset-splice-figure-s2

areas: dna-genomes
contexts: clinical_research
test count: 11047
original printed counts: N=11,047, %P=99.32%
source locator: Supplementary Figure S2 legend (page 21)
limitations: Figure 1 'Splice' has N=11,042; the five-variant difference is not explained, so the two splice AUROCs for the all-outputs scorer (0.592 and 0.614) are on different variant sets.

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