Proportion (gnomAD-set variants predicted pathogenic at the developer threshold) of PolyPhen-2 (Pejaver et al. 2022 calibration) on gnomAD reference set (Pejaver et al. 2022)
0.293 Proportion (gnomAD-set variants predicted pathogenic at the developer threshold)
Methods
- Tested configuration
- PolyPhen-2 (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)
- Procedure
- Share of gnomAD variants called pathogenic at developer thresholds (Pejaver et al. 2022 Table 3)
- Evaluation
- PolyPhen-2 at developer threshold 0.902: gnomAD fraction called pathogenic (Pejaver et al. 2022)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedPejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'PolyPhen-2', column 'Fraction of predicted pathogenic variants in the gnomAD set'
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 reference set
- Adaptation
- Developer-recommended pathogenicity threshold 0.902 (Table 3)
- Scoring implementation
- Fraction of variants at or beyond the threshold
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 0.293 Individual claims | Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Table 3, row 'PolyPhen-2', column 'Fraction of predicted pathogenic variants in the gnomAD set' 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 independent paper 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-devfraction-polyphen2
- metric
- proportion
- metric direction
- unknown
- unit
- fraction
- metric qualifier
- gnomAD-set variants predicted pathogenic at the developer threshold
- printed value
- 0.293
- numeric value
- 0.293
- denominator
- 363894
- source locator
- Table 3, row 'PolyPhen-2', column 'Fraction of predicted pathogenic variants in the gnomAD set'
- missing metadata
- uncertainty: reason: unreported
- 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.