Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) of VEST4 (Pejaver et al. 2022 calibration) on ClinVar 2019 calibration set (Pejaver et al. 2022)
[0.909, 0.964] Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025))
Methods
- Tested configuration
- VEST4 (Pejaver et al. 2022 calibration)
- Protocol
- PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1)
- Dataset
- ClinVar 2019 calibration set (Pejaver et al. 2022)
- Procedure
- PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1)
- Evaluation
- VEST4: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14).
- Evidence
- Author-reported evaluation · source checkedBergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'VEST4', column '(+3)'
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 [0.909, 0.964] Individual claims | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) Table 1, row 'VEST4', column '(+3)' Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | 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: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Original source · PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402
- 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-bergquist2025-vest4-plus3
- metric
- evidence-strength-score-interval
- metric direction
- unknown
- unit
- unitless
- unit detail
- VEST4 score
- metric qualifier
- PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)
- printed value
- [0.909, 0.964]
- numeric value
- 0.909
- source locator
- Table 1, row 'VEST4', column '(+3)'
- 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: 4fe954451167b5a5717a4c37f4054432e1f02fb59862d0fb909edb525e6bb8e2; retrieval url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12208618/; 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: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14).