Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3)
Local positive likelihood ratio, from the ClinVar 2019 posterior curves, at the default thresholds of SIFT, PolyPhen-2 and CADD, judged against the PP3 Supporting cut-off.
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
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All evaluations
3 evaluations · 3 results. Different protocols are not a single leaderboard.
Protocol: Local likelihood ratio at developer-recommended thresholds (Pejaver et al. 2022 Table 3) · Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)
Sorted by Likelihood ratio (local positive likelihood ratio at the developer threshold (0.050), PP3 Supporting requires 2.406) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Likelihood ratio (local positive likelihood ratio at the developer threshold (0.050), PP3 Supporting requires 2.406) | Likelihood ratio (local positive likelihood ratio at the developer threshold (0.902), PP3 Supporting requires 2.406) | Likelihood ratio (local positive likelihood ratio at the developer threshold (20.000), PP3 Supporting requires 2.406) |
|---|---|---|---|
| SIFT (Pejaver et al. 2022 calibration)Evaluation | 0.048 | Not reported | Not reported |
| CADD (Pejaver et al. 2022 calibration)Evaluation | Not reported | Not reported | 0.157 |
| PolyPhen-2 (Pejaver et al. 2022 calibration)Evaluation | Not reported | 1.99 | Not reported |
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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-protocol-pejaver2022-developer-threshold-lr
- areas
- dna-genomes
- contexts
- clinical_research
- protocol
- Read the local positive likelihood ratio at each tool's developer-recommended pathogenicity threshold and compare it with 2.406 (PP3 Supporting).
- task
- Evidence strength of developer thresholds
- metric
- likelihood-ratio
- metric direction
- higher
- unit
- unitless
- metric implementation
- Local positive likelihood ratio at the threshold with 95% bootstrap confidence interval
- version
- Pejaver et al. 2022, Table 3
- publication status
- peer_reviewed
- source locator
- Table 3 and footnote; Results 'Investigation of commonly used developer-recommended thresholds'
- limitations
- Calibration is genome-wide (average over genes); Tejura et al. 2024 report that about 70% of the gene-level REVEL and BayesDel intervals with enough control variants exceeded the number of incorrect predictions the genome-wide recommendations imply.; Labels are ClinVar classifications; the authors assume computational evidence had no major role in them (Stenton et al. 2024, Table 1).; Evidence strength was judged on the point estimate of the likelihood ratio (Table 3 footnote).
- 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; ai-assisted-source-review; method note: Checked against the Methods, table captions and author lists of the pinned sources.; note: Checked; see the dated review for rulings on origin and carried-over rows.
Related records
- part of: ClinGen SVI calibration of computational predictors for PP3/BP4
- uses data: ClinVar 2019 calibration set (Pejaver et al. 2022)
- assessed by: Use calibrated computational evidence for missense variants (PP3/BP4)
- assessment: CADD at developer threshold 20.000: local likelihood ratio (Pejaver et al. 2022)
- assessment: PolyPhen-2 at developer threshold 0.902: local likelihood ratio (Pejaver et al. 2022)
- assessment: SIFT at developer threshold 0.050: local likelihood ratio (Pejaver et al. 2022)