Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022)) of REVEL (Pejaver et al. 2022 calibration) on ClinVar 2019 calibration set (Pejaver et al. 2022)
(0.003, 0.016] Evidence strength score interval (BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022))
Methods
- Tested configuration
- REVEL (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)
- Procedure
- PP3/BP4 score intervals per evidence strength (Pejaver et al. 2022 Table 2)
- Evaluation
- REVEL: PP3/BP4 score intervals (Pejaver et al. 2022)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not yet extracted: One-sided confidence intervals are in Table S1, not retrieved
- Evidence
- Author-reported evaluation · source checkedPejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 2, row 'REVEL', column 'Benign (BP4): Strong'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Whole calibration set
- Adaptation
- None; thresholds fitted to the tool's scores
- Scoring implementation
- Local posterior probability of pathogenicity estimated in a sliding score window on the ClinVar 2019 set with prior 0.0441; a threshold is the most lenient score at which the one-sided 95% bootstrap bound (10,000 iterations) of the local positive likelihood ratio still reaches the cut-off for that strength (2.406, 5.790, 33.53, 1,124; reciprocals for BP4)
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result (0.003, 0.016] Individual claims | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 2, row 'REVEL', column 'Benign (BP4): Strong' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14T16:00:00Z author reported Audit detailsExtracted by extract/build_batch.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review. Field: Source artifact SHA-256: Hash scope: Exact downloaded bytes, before optional gzip storage Extraction artifact SHA-256: |
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-result-pejaver2022-revel-bp4-strong
- metric
- evidence-strength-score-interval
- metric direction
- unknown
- unit
- unitless
- unit detail
- REVEL score
- metric qualifier
- BP4 Strong, ClinGen SVI calibration (Pejaver et al. 2022)
- printed value
- (0.003, 0.016]
- numeric value
- 0.016
- source locator
- Table 2, row 'REVEL', column 'Benign (BP4): Strong'
- 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; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the source and matched the pinned SHA-256 (PMC page after blanking the two per-request tokens). review/check_values.py, written independently of the extractor, re-read the table and checked printed and numeric value, locator, metric, qualifier, unit, unit_detail, direction, uncertainty and the linked configuration, protocol and dataset; all 173 results matched.; note: Extracted by extract/build_batch.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review.
- numeric representation
- numeric_value is the bound a score must reach for this strength: the interval end further from the next-stronger interval
- missing metadata
- uncertainty: reason: unextracted; note: One-sided confidence intervals are in Table S1, not retrieved