Configuration

Variant-type pathogenicity prior on the benchmark's own labels (Lu et al. 2025)

Assigns each variant the frequency of pathogenic variants within its variant type, computed from the benchmark labels.

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Evaluations and results

2 evaluations · 2 results. Different protocols are not a single leaderboard.

Protocol: ClinVar pathogenic versus benign SNVs within variant type, AUROC (Lu et al. 2025)

Sorted by AUROC (ClinVar pathogenic vs benign SNVs, All variants) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUROC (ClinVar pathogenic vs benign SNVs, All variants)	AUROC (ClinVar pathogenic vs benign SNVs, Noncoding)
Variant-type pathogenicity prior on the benchmark's own labels (Lu et al. 2025)Evaluation	Lu et al. 2025 ClinVar benchmark: All variants (Figure 1)	0.962	Not reported
Variant-type pathogenicity prior on the benchmark's own labels (Lu et al. 2025)Evaluation	Lu et al. 2025 ClinVar benchmark: Noncoding (Figure 1)	Not reported	0.944

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Variant-type pathogenicity prior on the benchmark's own labels (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: All variants (Figure 1)	0.962 AUROC (ClinVar pathogenic vs benign SNVs, All variants) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Rule-based on ClinVar All variants 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 1, panel 1 'All variants (N=258,944, %P=30.59%)', row 'Rule-based', bar label
Configuration: Variant-type pathogenicity prior on the benchmark's own labels (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: Noncoding (Figure 1)	0.944 AUROC (ClinVar pathogenic vs benign SNVs, Noncoding) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Rule-based on ClinVar Noncoding 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 1, panel 2 'Noncoding (N=118,256, %P=10.69%)', row 'Rule-based', bar label

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

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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-config-variant-type-prior

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Rule-based
training overlap: Uses the benchmark's own labels to compute the per-type prior; an upper reference for type-only information, not a fair predictor.
source locator: Results paragraph 2 (page 6)

Related records

configuration of: Variant-type pathogenicity prior
system: Rule-based on ClinVar All variants SNVs (Lu et al. 2025 Figure 1)
system: Rule-based on ClinVar Noncoding SNVs (Lu et al. 2025 Figure 1)

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