Evidence claim

Baseline: Use calibrated computational evidence for missense variants (PP3/BP4)

Baseline of Use calibrated computational evidence for missense variants (PP3/BP4)

SIFT

Baseline method for the use case, drafted by the extraction agent; not reviewed.

Evidence

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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.

9 evidence rows 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
Claimed field baseline Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Method ids 1 values somatic-oncogenicity-20261009-method-sift Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.method_ids` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Pinned records 2 values record id use-case-missense-pp3-bp4-calibrated-evidence fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 25250cac852da67b4c4b8ff30fab89588ca97898bcad5ccea87d30e669fea4d1 record id vep-uc-20261014-source-pejaver2022 fields status attributes.artifact_sha256 sha256 c03d149f0fa601968241dc3dc7ece8cf2d8f55d81a2579b0a0fe4597190d77c9 Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Rationale SIFT is a conservation-based predictor that predates machine-learning ensembles; Pejaver et al. 2022 describe SIFT, PolyPhen-2 and CADD as among the first and most frequently used in silico tools, calibrate SIFT (Table 2) and test its developer threshold (Table 3). PolyPhen-2 and CADD are trained classifiers. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Source location vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Claimed value SIFT Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Description Baseline method for the use case, drafted by the extraction agent; not reviewed. Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Relationship: subject use-case-missense-pp3-bp4-calibrated-evidence Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `links:subject:use-case-missense-pp3-bp4-calibrated-evidence` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage
Name Baseline: Use calibrated computational evidence for missense variants (PP3/BP4) Context-only references	Pejaver et al. 2022, Am J Hum Genet 109:2163 (Europe PMC full text XML) Original source ↗ vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 3 Version: PMC9748256 (Am J Hum Genet 2022;109(12):2163) Retrieved: 2026-10-14T14:44:42Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `a78c7bcaacb0ccb72291264bbe7c1f9a16867b0c6207dcbb45c3c59a14af6b3b` Hash scope: Exact downloaded bytes, before optional gzip storage

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)

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Technical metadata and extraction receipts

Stable ID: use-case-baseline-missense-pp3-bp4-calibrated-evidence

field: baseline
value: SIFT
method ids: somatic-oncogenicity-20261009-method-sift
rationale: SIFT is a conservation-based predictor that predates machine-learning ensembles; Pejaver et al. 2022 describe SIFT, PolyPhen-2 and CADD as among the first and most frequently used in silico tools, calibrate SIFT (Table 2) and test its developer threshold (Table 3). PolyPhen-2 and CADD are trained classifiers.
source locator: vep-uc-20261014-source-pejaver2022: Results 'Investigation of commonly used developer-recommended thresholds'; Tables 2 and 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; method: ai-assisted-source-review; scope-review; method note: Checked the method record, the rationale and the cited source lines.; note: Baseline claim checked against docs/use-cases.md (best established pre-machine-learning method).
pins: record id: use-case-missense-pp3-bp4-calibrated-evidence; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 25250cac852da67b4c4b8ff30fab89588ca97898bcad5ccea87d30e669fea4d1; record id: vep-uc-20261014-source-pejaver2022; fields: status; attributes.artifact_sha256; sha256: c03d149f0fa601968241dc3dc7ece8cf2d8f55d81a2579b0a0fe4597190d77c9

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subject: Use calibrated computational evidence for missense variants (PP3/BP4)

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