Result

Likelihood ratio (local positive likelihood ratio at the developer threshold (0.050), PP3 Supporting requires 2.406) of SIFT (Pejaver et al. 2022 calibration) on ClinVar 2019 calibration set (Pejaver et al. 2022)

0.048 Likelihood ratio (local positive likelihood ratio at the developer threshold (0.050), PP3 Supporting requires 2.406)

Methods

Tested configuration: SIFT (Pejaver et al. 2022 calibration)
Protocol: Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3)
Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)
Procedure: Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3)
Evaluation: SIFT at developer threshold 0.050: local likelihood ratio (Pejaver et al. 2022)
Coverage: Not reported scored / Not reported eligible
Uncertainty: 95% CI 0.025 to 0.075. Calculated by the bootstrapping method (Table 3 footnote)
Evidence: Independent external evaluation · source checkedPejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) · Table 3, row 'SIFT', column 'lr +'

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: Developer-recommended pathogenicity threshold 0.050 (Table 3)
Scoring implementation: Local positive likelihood ratio at the threshold from the ClinVar 2019 posterior curve; 95% bootstrap interval

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 0.048 Individual claims	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ Table 3, row 'SIFT', column 'lr +' 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 independent paper 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-devlr-sift

metric: likelihood-ratio
metric direction: higher
unit: unitless
metric qualifier: local positive likelihood ratio at the developer threshold (0.050), PP3 Supporting requires 2.406
printed value: 0.048
numeric value: 0.048
printed source cell: 0.048 (0.025, 0.075)
uncertainty: type: confidence_interval; level: 0.95; lower: 0.025; upper: 0.075; printed: (0.025, 0.075); method: bootstrap; note: Calculated by the bootstrapping method (Table 3 footnote)
criterion: Evidence strength column: 'not met'
source locator: Table 3, row 'SIFT', column 'lr +'
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.

Related records

evaluation: SIFT at developer threshold 0.050: local likelihood ratio (Pejaver et al. 2022)

Suggest a correction