CADD (Pejaver et al. 2022 calibration)
CADD scores as calibrated by the ClinGen SVI Working Group in Pejaver et al. 2022.
Overview
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Evaluations and results
3 evaluations · 10 results. Different protocols are not a single leaderboard.
Sorted by Likelihood ratio (local positive likelihood ratio at the developer threshold (20.000), PP3 Supporting requires 2.406) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | Likelihood ratio (local positive likelihood ratio at the developer threshold (20.000), PP3 Supporting requires 2.406) | Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (BP4 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) | Evidence strength score interval (PP3 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) | Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CADD (Pejaver et al. 2022 calibration)Evaluation | Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3), ClinVar 2019 calibration set (Pejaver et al. 2022) | 0.157 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| CADD (Pejaver et al. 2022 calibration)Evaluation | PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2), ClinVar 2019 calibration set (Pejaver et al. 2022) | Not reported | (0.15, 17.3] | ≤0.15 | (17.3, 22.7] | – | ≥28.1 | – | [25.3, 28.1) | – | Not reported |
| CADD (Pejaver et al. 2022 calibration)Evaluation | Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3), gnomAD reference set (Pejaver et al. 2022) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.651 |
All 10 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CADD (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) | (0.15, 17.3] Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Benign (BP4): Moderate' |
| Configuration: CADD (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) | ≤0.15 Evidence strength score interval (BP4 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 | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Benign (BP4): Strong' |
| Configuration: CADD (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) | (17.3, 22.7] Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Benign (BP4): Supporting' |
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (BP4 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Benign (BP4): Very Strong' |
| Configuration: CADD (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) | ≥28.1 Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Pathogenic (PP3): Moderate' |
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (PP3 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Pathogenic (PP3): Strong' |
| Configuration: CADD (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) | [25.3, 28.1) Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Pathogenic (PP3): Supporting' |
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | – Evidence strength score interval (PP3 Very Strong, ClinGen SVI calibration (Pejaver et al. 2022)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD: 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 'CADD', column 'Pathogenic (PP3): Very Strong' |
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3) Dataset: gnomAD reference set (Pejaver et al. 2022) | 0.651 Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD at developer threshold 20.000: gnomAD fraction called pathogenic (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-gnomad-fraction Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'CADD', column 'Fraction of predicted pathogenic variants in the gnomAD set' |
| Configuration: CADD (Pejaver et al. 2022 calibration) | Protocol: Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022) | 0.157 Likelihood ratio (local positive likelihood ratio at the developer threshold (20.000), PP3 Supporting requires 2.406) unitless · higher Uncertainty: 95% CI 0.107 to 0.215. Calculated by the bootstrapping method (Table 3 footnote) Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCADD at developer threshold 20.000: local likelihood ratio (Pejaver et al. 2022) vep-uc-20261014-protocol-pejaver2022-developer-threshold-lr Aggregation: Not reported Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'CADD', column 'lr +' |
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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)
Technical metadata and extraction receipts
Stable ID: vep-uc-20261014-config-pejaver2022-cadd
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- supervised_machine_learning
- reported name
- CADD
- configuration type
- paper_evaluation
- foundation model eligible
- false
- version
- Scores generated by the authors; CADD 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
- No training-set removal stated for this tool (Methods lists BayesDel, FATHMM, MPC, MutPred2, PolyPhen-2, REVEL and VEST4)
- source locator
- Methods 'Tools' and 'Data sets'; Table 2 row 'CADD'
- 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.