Dataset

ClinVar 2019 calibration set (Pejaver et al. 2022)

ClinVar pathogenic, likely pathogenic, likely benign and benign missense variants used to calibrate predictor scores to ACMG/AMP evidence strengths.

Evaluation results

23 evaluations · 170 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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 checked Methods, coverage and source AlphaMissense: 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: BayesDel (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)	[−0.179, 0.129] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Indeterminate (0)'
Configuration: BayesDel (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)	[−0.359, −0.180] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Supporting (−1)'
Configuration: BayesDel (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)	[−0.519, −0.360] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Moderate (−2)'
Configuration: BayesDel (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)	≤ −0.520 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column '(−3)'
Configuration: BayesDel (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)	- 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Strong (−4)'
Configuration: BayesDel (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)	[0.130, 0.269] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Supporting (+1)'
Configuration: BayesDel (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)	[0.270, 0.409] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Moderate (+2)'
Configuration: BayesDel (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)	[0.410, 0.499] 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column '(+3)'
Configuration: BayesDel (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)	≥ 0.5 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 checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Strong (+4)'
Configuration: ESM1b (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)	[−10.6, −6.4] 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Indeterminate (0)'
Configuration: ESM1b (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)	[−6.3, −3.2] 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Supporting (−1)'
Configuration: ESM1b (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)	[−3.1, 8.7] 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Moderate (−2)'
Configuration: ESM1b (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)	≥ 8.8 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column '(−3)'
Configuration: ESM1b (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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Strong (−4)'
Configuration: ESM1b (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)	[−12.1, −10.7] 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Supporting (+1)'
Configuration: ESM1b (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)	[−13.9, −12.2] 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 checked Methods, coverage and source ESM1b: 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 'ESM1b', column 'Moderate (+2)'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Research readiness

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.

Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

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.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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.

9 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Access Supplementary Data S1 (Excel), not retrieved in this pass. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.access` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Label semantics Positive: ClinVar pathogenic or likely pathogenic. Negative: ClinVar benign or likely benign. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.label_semantics` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Population 11,834 missense variants from 1,914 genes: allele frequency below 0.01 in gnomAD v2.1, genes with at least one pathogenic variant of any type in ClinVar, VUS, zero-star and conflicting entries removed, and variants in the training sets of BayesDel, FATHMM, MPC, MutPred2, PolyPhen-2, REVEL and VEST4 (and constituent tools of the meta-predictors) removed where available. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Source location Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Species Homo sapiens Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.species` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Split Whole set used for calibration; the ClinVar 2020 set (9,114 variants from 2,197 genes, submitted after December 2019) is the separate test set Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Version ClinVar VCF downloaded December 2019, filtered as in Figure 1A Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Description ClinVar pathogenic, likely pathogenic, likely benign and benign missense variants used to calibrate predictor scores to ACMG/AMP evidence strengths. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Name ClinVar 2019 calibration set (Pejaver et al. 2022) Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Original source · PMC9748256 (Am J Hum Genet 2022;109(12):2163)

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Technical metadata and extraction receipts

Stable ID: vep-uc-20261014-dataset-pejaver2022-clinvar2019

areas: dna-genomes
contexts: clinical_research
version: ClinVar VCF downloaded December 2019, filtered as in Figure 1A
split: Whole set used for calibration; the ClinVar 2020 set (9,114 variants from 2,197 genes, submitted after December 2019) is the separate test set
population: 11,834 missense variants from 1,914 genes: allele frequency below 0.01 in gnomAD v2.1, genes with at least one pathogenic variant of any type in ClinVar, VUS, zero-star and conflicting entries removed, and variants in the training sets of BayesDel, FATHMM, MPC, MutPred2, PolyPhen-2, REVEL and VEST4 (and constituent tools of the meta-predictors) removed where available.
label semantics: Positive: ClinVar pathogenic or likely pathogenic. Negative: ClinVar benign or likely benign.
species: Homo sapiens
access: Supplementary Data S1 (Excel), not retrieved in this pass.
source locator: Methods 'Data sets: The ClinVar 2019 set'; Figure 1A; Data and code availability
review: reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T16:00:00Z; artifact sha256: a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9748256/fullTextXML; method: source-hash-verification; ai-assisted-source-review; method note: Checked against the Methods, table captions and author lists of the pinned sources.; note: Checked; see the dated review for rulings on origin and carried-over rows.

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