Published calibration; transcribed, not reproduced.
1 evaluation · 9 results. Different protocols are not a single leaderboard.
Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) · 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 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (Indeterminate (0 points), ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (PP3 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) | Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) |
|---|---|---|---|---|---|---|---|---|---|
| MutPred2 (Pejaver et al. 2022 calibration)Evaluation | [0.011, 0.031] | [0.032, 0.197] | ≤ 0.01 | [0.198, 0.391] | [0.392, 0.736] | [0.895, 0.931] | [0.829, 0.894] | ≥ 0.932 | [0.737, 0.828] |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.392, 0.736] Evidence strength score interval (Indeterminate (0 points), ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Indeterminate (0)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.198, 0.391] Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Supporting (−1)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.032, 0.197] Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Moderate (−2)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.011, 0.031] Evidence strength score interval (BP4 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column '(−3)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | ≤ 0.01 Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Strong (−4)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.737, 0.828] Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Supporting (+1)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.829, 0.894] Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Moderate (+2)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | [0.895, 0.931] Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column '(+3)' |
| Configuration: MutPred2 (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | ≥ 0.932 Evidence strength score interval (PP3 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'MutPred2', column 'Strong (+4)' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified
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PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1)
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
38 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| 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 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded author reported 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| 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 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Comparison: budget Not reported Context-only references | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Comparison: budget Not reported Context-only references | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | missing or unspecified No individual claim review recorded author reported 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| 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 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded author reported 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| 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 1, row 'MutPred2' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | not individually reviewed No individual claim review recorded author reported 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-bergquist2025-intervals-mutpred2