PrimateAI (Pejaver et al. 2022 calibration)
PrimateAI scores as calibrated by the ClinGen SVI Working Group in Pejaver et al. 2022.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 8 results. Different protocols are not a single leaderboard.
Protocol: PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) · 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 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)) |
|---|---|---|---|---|---|---|---|---|
| PrimateAI (Pejaver et al. 2022 calibration)Evaluation | ≤0.362 | – | (0.362, 0.483] | – | ≥0.867 | – | [0.790, 0.867) | – |
All 8 result rows with coverage, uncertainty and sources
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: PrimateAI (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) | ≤0.362 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 sourcePrimateAI: 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 'PrimateAI', column 'Benign (BP4): Moderate' |
| Configuration: PrimateAI (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 | Independent external evaluation · Source checkedMethods, coverage and sourcePrimateAI: 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 'PrimateAI', column 'Benign (BP4): Strong' |
| Configuration: PrimateAI (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) | (0.362, 0.483] 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 sourcePrimateAI: 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 'PrimateAI', column 'Benign (BP4): Supporting' |
| Configuration: PrimateAI (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 sourcePrimateAI: 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 'PrimateAI', column 'Benign (BP4): Very Strong' |
| Configuration: PrimateAI (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) | ≥0.867 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 sourcePrimateAI: 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 'PrimateAI', column 'Pathogenic (PP3): Moderate' |
| Configuration: PrimateAI (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 sourcePrimateAI: 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 'PrimateAI', column 'Pathogenic (PP3): Strong' |
| Configuration: PrimateAI (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) | [0.790, 0.867) 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 sourcePrimateAI: 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 'PrimateAI', column 'Pathogenic (PP3): Supporting' |
| Configuration: PrimateAI (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 sourcePrimateAI: 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 'PrimateAI', column 'Pathogenic (PP3): Very Strong' |
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Evidence
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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-primateai
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- supervised_machine_learning
- reported name
- PrimateAI
- configuration type
- paper_evaluation
- foundation model eligible
- false
- version
- Precomputed scores from dbNSFP (version not stated in the main text; reference 26 is dbNSFP v4)
- 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 'PrimateAI'
- 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: PrimateAI
- system: PrimateAI: PP3/BP4 score intervals (Pejaver et al. 2022)