Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML)
PMC9748256 (Am J Hum Genet 2022;109(12):2163) · Peer-reviewed
What this source contributed
Records in this release that cite this source. A record can cite several sources.
Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Claims
Statements this source supports, each with where in the source it was checked.
- Baseline: Use calibrated computational evidence for missense variants (PP3/BP4): Baseline SIFT (vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3)
- Relevance of vep-uc-20261014-protocol-bergquist2025-point-intervals to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) (vep-uc-20261014-source-bergquist2025: Table 1 and caption; Materials and Methods; Results; vep-uc-20261014-source-tejura2024: Summary)
- Relevance of vep-uc-20261014-protocol-pejaver2022-developer-threshold-gnomad-fraction to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3) (vep-uc-20261014-source-pejaver2022: Table 3 last column; Results 'Investigation of commonly used developer-recommended thresholds')
- Relevance of vep-uc-20261014-protocol-pejaver2022-developer-threshold-lr to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3) (vep-uc-20261014-source-pejaver2022: Table 3 and footnote; Results 'Investigation of commonly used developer-recommended thresholds')
- Relevance of vep-uc-20261014-protocol-pejaver2022-intervals to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2) (vep-uc-20261014-source-pejaver2022: Table 2 and footnote; Methods; author list; references 13, 18, 19, 23, 25; vep-uc-20261014-source-tejura2024: Summary; vep-uc-20261014-source-stenton2024: Table 1)
Models, benchmarks and other records
Configurations (13)
- BayesDel (Pejaver et al. 2022 calibration)
- CADD (Pejaver et al. 2022 calibration)
- EA (Pejaver et al. 2022 calibration)
- FATHMM (Pejaver et al. 2022 calibration)
- GERP++ (Pejaver et al. 2022 calibration)
- MPC (Pejaver et al. 2022 calibration)
- MutPred2 (Pejaver et al. 2022 calibration)
- PhyloP (Pejaver et al. 2022 calibration)
- PolyPhen-2 (Pejaver et al. 2022 calibration)
- PrimateAI (Pejaver et al. 2022 calibration)
- REVEL (Pejaver et al. 2022 calibration)
- SIFT (Pejaver et al. 2022 calibration)
- VEST4 (Pejaver et al. 2022 calibration)
Benchmarks (1)
Protocols (4)
- Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3)
- PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1)
- PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2)
- Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3)
Datasets (2)
Evaluations (23)
- BayesDel: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- BayesDel: PP3/BP4 score intervals (Pejaver et al. 2022)
- CADD at developer threshold 20.000: gnomAD fraction called pathogenic (Pejaver et al. 2022)
- CADD at developer threshold 20.000: local likelihood ratio (Pejaver et al. 2022)
- CADD: PP3/BP4 score intervals (Pejaver et al. 2022)
- EA: PP3/BP4 score intervals (Pejaver et al. 2022)
- FATHMM: PP3/BP4 score intervals (Pejaver et al. 2022)
- GERP++: PP3/BP4 score intervals (Pejaver et al. 2022)
- MPC: PP3/BP4 score intervals (Pejaver et al. 2022)
- MutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- MutPred2: PP3/BP4 score intervals (Pejaver et al. 2022)
- PhyloP: PP3/BP4 score intervals (Pejaver et al. 2022)
- PolyPhen-2 at developer threshold 0.902: gnomAD fraction called pathogenic (Pejaver et al. 2022)
- PolyPhen-2 at developer threshold 0.902: local likelihood ratio (Pejaver et al. 2022)
- PolyPhen2: PP3/BP4 score intervals (Pejaver et al. 2022)
- PrimateAI: PP3/BP4 score intervals (Pejaver et al. 2022)
- REVEL: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- REVEL: PP3/BP4 score intervals (Pejaver et al. 2022)
- SIFT at developer threshold 0.050: gnomAD fraction called pathogenic (Pejaver et al. 2022)
- SIFT at developer threshold 0.050: local likelihood ratio (Pejaver et al. 2022)
- SIFT: PP3/BP4 score intervals (Pejaver et al. 2022)
- VEST4: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- VEST4: PP3/BP4 score intervals (Pejaver et al. 2022)
Use cases (1)
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.
27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Doi 10.1016/j.ajhg.2022.10.013 Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Hash scope Exact downloaded bytes, before optional gzip storage Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Licence CC BY 4.0 Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
Limitations2 values
| Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Media type application/xml Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Publication status peer_reviewed Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Retrieved at 2026-10-14T14:44:42Z Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| attributes.review.artifact_sha256 a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
| Review: method note Re-downloaded on 2026-10-14 and matched the pinned SHA-256 (PMC pages after blanking the ncbi_phid and csrfmiddlewaretoken values, checked by an independent normaliser). Source metadata | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) No field-specific location recorded Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
ClinGen Sequence Variant Interpretation Working Group calibration of 13 missense predictors to ACMG/AMP PP3 and BP4 evidence strengths, with score thresholds per strength and a check of developer-recommended thresholds.
Technical metadata and extraction receipts
Stable ID: vep-uc-20261014-source-pejaver2022
- areas
- dna-genomes
- contexts
- clinical_research
- url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9748256/fullTextXML
- version
- PMC9748256 (Am J Hum Genet 2022;109(12):2163)
- retrieved at
- 2026-10-14T14:44:42Z
- artifact sha256
- a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b
- publication status
- peer_reviewed
- licence
- CC BY 4.0
- source locator
- Methods 'Data sets', 'Estimation of the prevalence of pathogenic variants', 'Statistical framework'; Tables 1-4; Declaration of interests; Data and code availability
- doi
- 10.1016/j.ajhg.2022.10.013
- hash scope
- Exact downloaded bytes, before optional gzip storage
- media type
- application/xml
- limitations
- Table S1 (point estimates and one-sided confidence intervals behind Table 2) is in the supplement, which was not retrieved.; Thresholds are estimated genome-wide; the Discussion notes that evidence strength can differ between genes.
- 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; method note: Re-downloaded on 2026-10-14 and matched the pinned SHA-256 (PMC pages after blanking the ncbi_phid and csrfmiddlewaretoken values, checked by an independent normaliser).; note: Hash matches.