Configuration

BayesDel (Pejaver et al. 2022 calibration)

BayesDel scores as calibrated by the ClinGen SVI Working Group in Pejaver et al. 2022.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

2 evaluations · 17 results. Different protocols are not a single leaderboard.

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	Protocol and dataset	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 (Pejaver et al. 2022))	Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022))	Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration (Pejaver et al. 2022))	Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022))	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 (Pejaver et al. 2022))	Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Strong, ClinGen SVI calibration (Pejaver et al. 2022))	Evidence strength score interval (PP3 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration (Pejaver et al. 2022))	Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022))
BayesDel (Pejaver et al. 2022 calibration)Evaluation	PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1)	≤ −0.520	Not reported	[−0.519, −0.360]	Not reported	-	Not reported	[−0.359, −0.180]	Not reported	[−0.179, 0.129]	[0.410, 0.499]	Not reported	[0.270, 0.409]	Not reported	≥ 0.5	Not reported	[0.130, 0.269]	Not reported
BayesDel (Pejaver et al. 2022 calibration)Evaluation	PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2)	Not reported	≤ −0.36	Not reported	–	Not reported	(−0.36, −0.18]	Not reported	–	Not reported	Not reported	[0.27, 0.50)	Not reported	≥0.5	Not reported	[0.13, 0.27)	Not reported	–

All 17 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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: BayesDel (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)	≤ −0.36 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Benign (BP4): Moderate'
Configuration: BayesDel (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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Benign (BP4): Strong'
Configuration: BayesDel (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)	(−0.36, −0.18] 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Benign (BP4): Supporting'
Configuration: BayesDel (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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Benign (BP4): Very Strong'
Configuration: BayesDel (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)	[0.27, 0.50) 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Pathogenic (PP3): Moderate'
Configuration: BayesDel (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)	≥0.5 Evidence strength score interval (PP3 Strong, 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Pathogenic (PP3): Strong'
Configuration: BayesDel (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)	[0.13, 0.27) 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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Pathogenic (PP3): Supporting'
Configuration: BayesDel (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	Author-reported evaluation · Source checked Methods, coverage and source BayesDel: 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 'BayesDel', column 'Pathogenic (PP3): Very Strong'

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

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

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

1 source record and release history

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)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: vep-uc-20261014-config-pejaver2022-bayesdel

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: BayesDel
configuration type: paper_evaluation
foundation model eligible: false
version: BayesDel without minor allele frequency (scores generated by the authors; release not stated)
access reuse: Scores obtained by Pejaver et al. 2022 (Methods 'Tools'); calibration code at https://github.com/vpejaver/clingen-svi-comp_calibration
score training overlap: Variants in this tool's training set (and its constituents') were removed from the calibration data where available (Methods)
source locator: Methods 'Tools' and 'Data sets'; Table 2 row 'BayesDel'
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.

Related records

configuration of: BayesDel
system: BayesDel: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
system: BayesDel: PP3/BP4 score intervals (Pejaver et al. 2022)

Suggest a correction