Published calibration; transcribed, not reproduced.
1 evaluation · 8 results. Different protocols are not a single leaderboard.
Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) · Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)
In source order. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) |
|---|---|---|---|---|---|---|---|---|
| FATHMM (Pejaver et al. 2022 calibration)Evaluation | ≥4.69 | – | [3.32, 4.69) | – | ≤ −5.04 | – | (−5.04, −4.14] | – |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | ≥4.69 Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Benign (BP4): Moderate' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Benign (BP4): Strong' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [3.32, 4.69) Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Benign (BP4): Supporting' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (BP4 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Benign (BP4): Very Strong' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | ≤ −5.04 Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Pathogenic (PP3): Moderate' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (PP3 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Pathogenic (PP3): Strong' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | (−5.04, −4.14] Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Pathogenic (PP3): Supporting' |
| Configuration: FATHMM (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (PP3 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFATHMM: PP3/BP4 score intervals (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-intervals Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'FATHMM', column 'Pathogenic (PP3): Very Strong' |
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PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2)
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17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation None; thresholds fitted to the tool's scores Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 2, row 'FATHMM' 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 2, row 'FATHMM' 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 2, row 'FATHMM' 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 2, row 'FATHMM' 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 2, row 'FATHMM' 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 posterior probability of pathogenicity estimated in a sliding score window on the ClinVar 2019 set with prior 0.0441; a threshold is the most lenient score at which the one-sided 95% bootstrap bound (10,000 iterations) of the local positive likelihood ratio still reaches the cut-off for that strength (2.406, 5.790, 33.53, 1,124; reciprocals for BP4) Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 2, row 'FATHMM' 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 2, row 'FATHMM' 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-intervals Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 2, row 'FATHMM' 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 2, row 'FATHMM' 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 2, row 'FATHMM' 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-intervals-fathmm