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)) |
|---|---|---|---|---|---|---|---|---|---|
| AlphaMissense (Bergquist et al. 2025 calibration)Evaluation | ≤ 0.07 | [0.071, 0.099] | - | [0.100, 0.169] | [0.170, 0.791] | [0.972, 0.989] | [0.906, 0.971] | ≥ 0.99 | [0.792, 0.905] |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.170, 0.791] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Indeterminate (0)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.100, 0.169] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Supporting (−1)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.071, 0.099] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Moderate (−2)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | ≤ 0.07 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column '(−3)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | - Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Strong (−4)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.792, 0.905] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Supporting (+1)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.906, 0.971] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column 'Moderate (+2)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | [0.972, 0.989] 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', column '(+3)' |
| Configuration: AlphaMissense (Bergquist et al. 2025 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) | ≥ 0.99 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 | Independent external evaluation · Source checkedMethods, coverage and sourceAlphaMissense: 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 'AlphaMissense', 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
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
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.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | missing or unspecified No individual claim review recorded independent paper 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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: 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 | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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: population 11,834 missense variants from 1,914 genes; prior probability of pathogenicity 4.41% (gnomAD set) Context-only references | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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: protocol id vep-uc-20261014-protocol-bergquist2025-point-intervals Context-only references | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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: split Whole calibration set Context-only references | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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. |
| Origin independent_paper Context-only references | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'AlphaMissense' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | not individually reviewed No individual claim review recorded independent paper 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. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: vep-uc-20261014-eval-bergquist2025-intervals-alphamissense