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1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: PolyPhen-2 (Pejaver et al. 2022 calibration) | Protocol: Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | 1.99 Likelihood ratio (local positive likelihood ratio at the developer threshold (0.902), PP3 Supporting requires 2.406) unitless · higher Uncertainty: 95% CI 1.560 to 2.492. Calculated by the bootstrapping method (Table 3 footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcePolyPhen-2 at developer threshold 0.902: local likelihood ratio (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-lr Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'PolyPhen-2', column 'lr +' |
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Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3)
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17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Developer-recommended pathogenicity threshold 0.902 (Table 3) Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: aggregation Pooled over variants in all genes Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: budget Not reported Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: dataset version ClinVar December 2019, filtered (Figure 1A) Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: inputs Precomputed or author-generated scores of the tool for each variant Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: metric implementation Local positive likelihood ratio at the threshold from the ClinVar 2019 posterior curve; 95% bootstrap interval Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: population 11,834 missense variants from 1,914 genes; prior probability of pathogenicity 4.41% (gnomAD set) Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: protocol id vep-uc-20261014-protocol-pejaver2022-developer-threshold-lr Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: split Whole calibration set Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Origin independent_paper Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: vep-uc-20261014-eval-pejaver2022-devlr-polyphen2