Result

Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)) of VEST4 (Pejaver et al. 2022 calibration) on ClinVar 2019 calibration set (Pejaver et al. 2022)

≤0.302 Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022))

Methods

Tested configuration: VEST4 (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: VEST4: 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 'VEST4', column 'Benign (BP4): Moderate'

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

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Reported result ≤0.302 Individual claims	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Table 2, row 'VEST4', column 'Benign (BP4): Moderate' Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14T16:00:00Z author reported Audit details Extracted by extract/build_batch.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review. Field: `attributes.printed_value` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage Extraction artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Extraction artifact

How to read the evidence

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)

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: vep-uc-20261014-result-pejaver2022-vest4-bp4-moderate

metric: evidence-strength-score-interval
metric direction: unknown
unit: unitless
unit detail: VEST4 score
metric qualifier: BP4 Moderate, ClinGen SVI calibration (Pejaver et al. 2022)
printed value: ≤0.302
numeric value: 0.302
source locator: Table 2, row 'VEST4', column 'Benign (BP4): Moderate'
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 printed bound
missing metadata: uncertainty: reason: unextracted; note: One-sided confidence intervals are in Table S1, not retrieved

Related records

evaluation: VEST4: PP3/BP4 score intervals (Pejaver et al. 2022)

Suggest a correction