Dataset subset

Lu et al. 2025 ClinVar benchmark: RNA gene (Figure 1)

ClinVar SNVs in the 'RNA gene' group of the Lu et al. 2025 benchmark, restricted to variants scored by every model in the panel.

Evaluation results

7 evaluations · 7 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

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: RNA gene (Figure 1)	0.851 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) 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 on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'AlphaGenome', bar label
Configuration: DNABERT-2 117M, CLS embedding L2 distance (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: RNA gene (Figure 1)	0.423 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DNABERT2 on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'DNABERT2', bar label
Configuration: Evo 2 7B base, 8,192 bp log-likelihood ratio (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: RNA gene (Figure 1)	0.459 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Evo2 on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'Evo2', bar label
Configuration: GPN-MSA precomputed hg38 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: RNA gene (Figure 1)	0.938 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source GPN-MSA on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'GPN-MSA', bar label
Configuration: Nucleotide Transformer 2.5B multi-species, CLS embedding L2 distance (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: RNA gene (Figure 1)	0.371 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Nucleotide Transformer on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'Nucleotide Transformer', bar label
Configuration: PhyloGPN, official example code (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: RNA gene (Figure 1)	0.476 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhyloGPN on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'PhyloGPN', bar label
Configuration: PhyloP 100-way vertebrate (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: RNA gene (Figure 1)	0.882 AUROC (ClinVar pathogenic vs benign SNVs, RNA gene) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source PhyloP on ClinVar RNA gene SNVs (Lu et al. 2025 Figure 1) 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) · Figure 1 (page 8), column 2, panel 2 'RNA gene (N=131, %P=25.95%)', row 'PhyloP', bar label

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

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Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Verified: Not verified

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Verified: Not verified

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Subset and evaluation context

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Evidence

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Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

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
Original printed counts N=131, %P=25.95% Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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 Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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 131 Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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 SNVs in the 'RNA gene' group of the Lu et al. 2025 benchmark, restricted to variants scored by every model in the panel. Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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: 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 ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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: RNA gene (Figure 1) Context-only references	Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Original source ↗ Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)' 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

How to read the evidence

Sources and history

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-rna-gene

areas: dna-genomes
contexts: clinical_research
test count: 131
original printed counts: N=131, %P=25.95%
source locator: Figure 1 (page 8), column 2, panel 2, title 'RNA gene (N=131, %P=25.95%)'

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