ClinVar GRCh38 germline SNVs with definitive pathogenic or benign labels, grouped by variant type from MANE RefSeq and ClinVar HGVS annotations.
No reviewed evaluations of this dataset are linked in this release.
0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.
Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
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8 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population 259,600 SNVs (Supplementary Figure S1); 258,944 scored in Figure 1 'All variants', 30.59% pathogenic Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Repository https://github.com/Brandes-Lab/VEP-eval Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Source location Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Split None: all models are zero-shot or precomputed; no training on the benchmark Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Variant count 259600 Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Version ClinVar variant_summary release 2025-03-31; MANE RefSeq v1.4 GFF Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Description ClinVar GRCh38 germline SNVs with definitive pathogenic or benign labels, grouped by variant type from MANE RefSeq and ClinVar HGVS annotations. Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Name Lu et al. 2025 ClinVar SNV variant-type benchmark (259,600 SNVs) Context-only references | Genomic heterogeneity inflates the performance of variant pathogenicity predictions (Lu, Liu, Lin and Brandes, bioRxiv 2025, v2) Methods 'ClinVar benchmark preparation' (pages 11 to 12); Supplementary Figure S1 (page 20) Version: bioRxiv preprint version 2, posted 2025-09-10 (version 1 posted 2025-09-08); full-text PDF (21 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: lu-hetero-20261019-data-clinvar-snv-benchmark