Evidence claim

Relevance of vep-lit-20261014-protocol-livesey2025-dms-indirect to use-case-missense-pp3-bp4-calibrated-evidence

Use case: Use calibrated computational evidence for missense variants (PP3/BP4)
Assessed by: Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only
Relevance: Proxy evidence
Endpoint: Average pairwise win rate by |Spearman| with the DMS assays the authors class as indirect

Relevance judgement drafted by the extraction agent; independently reviewed, automated review only.

97 reviewed evaluations

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.

19 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
Citation locations 1 values source id vep-lit-20261014-source-livesey2025-supplementary-2 locator Supplementary Material 2 Table S5; Results Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison group livesey-marsh-2025-vep-ranking Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison title Livesey and Marsh 2025 VEP rankings Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results. Compare rows only within this protocol. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Endpoint Average pairwise win rate by \|Spearman\| with the DMS assays the authors class as indirect Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Claimed field links:assessed_by:vep-lit-20261014-protocol-livesey2025-dms-indirect Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Headline metric pairwise-win-rate Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Limitations 4 values Which assays are indirect is not fully recoverable from Table S1. No calibration to ACMG/AMP evidence strength and no thresholds. Correlation is assessed within each protein, so the ranking does not test whether scores are comparable across genes; the authors report that DMS and clinical rankings agree closely for population-free and population-tuned VEPs (Pearson r 0.978 and 0.994) and less for clinical-trained VEPs (Results, Fig. 4). Transcribed from the source; no reproduction by Rewire and no human scientific review. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Pinned records 198 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-lit-20261014-eval-livesey2025-dms-indirect-3cnet fields status links attributes.origin attributes.comparison sha256 1f9739ad7b916a0e731c7438c164bf2d1ea952f799fac565ae9929ab5c9ab24a record id vep-lit-20261014-eval-livesey2025-dms-indirect-alphamissense fields status links attributes.origin attributes.comparison sha256 426aeb85e3ce464442724e97753335bb3d2d5e93fd605e9b61e352c3a6f2a59d record id vep-lit-20261014-eval-livesey2025-dms-indirect-alphscore fields status links attributes.origin attributes.comparison sha256 ecc3feb01ecdbc61f5ccb99722282b5af40f2275253c4170fb072a93f2004bd2 record id 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attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 bac4290be60d551e0a6605843289304cb05e039475ec795b80744abf6ed51850 record id vep-lit-20261014-result-livesey2025-dms-indirect-wavenet-rank-score-indirect fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 90b8954361849d192c71b7b2dc81930ffa8521662d93767d8c17c2555d5a6ebe record id vep-lit-20261014-source-livesey2025-article fields status attributes.artifact_sha256 sha256 93fc887334181cc257a844dbee3d027cb1ec229053eebf132d3d6a563fce63c1 record id vep-lit-20261014-source-livesey2025-supplementary-2 fields status attributes.artifact_sha256 sha256 654913943e661a8ff6fba0bccdcdaaebf17cf0bb54a9e6f39ddffd5b248c330d Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Rationale Proxy: DMS-based ranking avoids clinical-label circularity, which the calibrations cannot fully remove, and so is an independent check on which predictors to calibrate; it gives no thresholds or evidence strengths. Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record

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Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141

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Stable ID: use-case-mapping-vep-uc-20261014-missense-pp3-bp4-calibrated-evidence-livesey2025-dms-indirect

field: links:assessed_by:vep-lit-20261014-protocol-livesey2025-dms-indirect
value: vep-lit-20261014-protocol-livesey2025-dms-indirect
relevance: proxy
endpoint: Average pairwise win rate by |Spearman| with the DMS assays the authors class as indirect
rationale: Proxy: DMS-based ranking avoids clinical-label circularity, which the calibrations cannot fully remove, and so is an independent check on which predictors to calibrate; it gives no thresholds or evidence strengths.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results.; Compare rows only within this protocol.
limitations: Which assays are indirect is not fully recoverable from Table S1.; No calibration to ACMG/AMP evidence strength and no thresholds.; Correlation is assessed within each protein, so the ranking does not test whether scores are comparable across genes; the authors report that DMS and clinical rankings agree closely for population-free and population-tuned VEPs (Pearson r 0.978 and 0.994) and less for clinical-trained VEPs (Results, Fig. 4).; Transcribed from the source; no reproduction by Rewire and no human scientific review.
citation locators: source id: vep-lit-20261014-source-livesey2025-supplementary-2; locator: Supplementary Material 2 Table S5; Results
source locator: vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results
headline metric: pairwise-win-rate
comparison group: livesey-marsh-2025-vep-ranking
comparison title: Livesey and Marsh 2025 VEP rankings
stratum label: DMS benchmark, indirect assays only
stratum order: 3
reason: VEP use-case pass 2026-10-14: relevance of a protocol to a new use case (rewire-benchmark-data #151/#152).
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 endpoint against the use case's question, inputs, exclusions and output; checked each limitation and number against the cited sources, re-downloaded and hash-matched; listed every evaluation on the protocol in reviewed_evaluations (values of evaluations already in the store were checked by their own independent reviews).; note: Judgement drafted by the extraction agent and revised in review (docs/reviews/vep-use-cases-2026-10-14-review.md).
reviewed evaluations: vep-lit-20261014-eval-livesey2025-dms-indirect-3cnet; vep-lit-20261014-eval-livesey2025-dms-indirect-alphamissense; vep-lit-20261014-eval-livesey2025-dms-indirect-alphscore; vep-lit-20261014-eval-livesey2025-dms-indirect-bayesdel; vep-lit-20261014-eval-livesey2025-dms-indirect-bayesdel-noaf; vep-lit-20261014-eval-livesey2025-dms-indirect-blosum62; vep-lit-20261014-eval-livesey2025-dms-indirect-cadd-1-6; vep-lit-20261014-eval-livesey2025-dms-indirect-cadd-1-7; vep-lit-20261014-eval-livesey2025-dms-indirect-capice; vep-lit-20261014-eval-livesey2025-dms-indirect-carp; vep-lit-20261014-eval-livesey2025-dms-indirect-clinpred; vep-lit-20261014-eval-livesey2025-dms-indirect-condel; vep-lit-20261014-eval-livesey2025-dms-indirect-cpt-1; vep-lit-20261014-eval-livesey2025-dms-indirect-dann; vep-lit-20261014-eval-livesey2025-dms-indirect-deepsav; vep-lit-20261014-eval-livesey2025-dms-indirect-deepsequence; vep-lit-20261014-eval-livesey2025-dms-indirect-demask; vep-lit-20261014-eval-livesey2025-dms-indirect-deogen2; vep-lit-20261014-eval-livesey2025-dms-indirect-eigen; vep-lit-20261014-eval-livesey2025-dms-indirect-envision; vep-lit-20261014-eval-livesey2025-dms-indirect-escott; vep-lit-20261014-eval-livesey2025-dms-indirect-esm-1b; vep-lit-20261014-eval-livesey2025-dms-indirect-esm-1v; vep-lit-20261014-eval-livesey2025-dms-indirect-esm2; vep-lit-20261014-eval-livesey2025-dms-indirect-eve; vep-lit-20261014-eval-livesey2025-dms-indirect-evmutation-epistatic; vep-lit-20261014-eval-livesey2025-dms-indirect-evmutation-independent; vep-lit-20261014-eval-livesey2025-dms-indirect-fathmm; vep-lit-20261014-eval-livesey2025-dms-indirect-fathmm-mkl; vep-lit-20261014-eval-livesey2025-dms-indirect-fathmm-xf; vep-lit-20261014-eval-livesey2025-dms-indirect-fitcons; vep-lit-20261014-eval-livesey2025-dms-indirect-gemme; vep-lit-20261014-eval-livesey2025-dms-indirect-genocanyon; vep-lit-20261014-eval-livesey2025-dms-indirect-gerp-plus-plus; vep-lit-20261014-eval-livesey2025-dms-indirect-gmvp; vep-lit-20261014-eval-livesey2025-dms-indirect-grantham; vep-lit-20261014-eval-livesey2025-dms-indirect-igemme; vep-lit-20261014-eval-livesey2025-dms-indirect-inmerf; vep-lit-20261014-eval-livesey2025-dms-indirect-lassie; vep-lit-20261014-eval-livesey2025-dms-indirect-list-s2; vep-lit-20261014-eval-livesey2025-dms-indirect-lrt; vep-lit-20261014-eval-livesey2025-dms-indirect-m-cap; vep-lit-20261014-eval-livesey2025-dms-indirect-maverick-benign; vep-lit-20261014-eval-livesey2025-dms-indirect-metalr; vep-lit-20261014-eval-livesey2025-dms-indirect-metarnn; vep-lit-20261014-eval-livesey2025-dms-indirect-metasvm; vep-lit-20261014-eval-livesey2025-dms-indirect-mistic; vep-lit-20261014-eval-livesey2025-dms-indirect-moipred-benign; vep-lit-20261014-eval-livesey2025-dms-indirect-mpc; vep-lit-20261014-eval-livesey2025-dms-indirect-msa-transformer; vep-lit-20261014-eval-livesey2025-dms-indirect-mutationassessor; vep-lit-20261014-eval-livesey2025-dms-indirect-mutationtcn; vep-lit-20261014-eval-livesey2025-dms-indirect-mutformer; vep-lit-20261014-eval-livesey2025-dms-indirect-mutpred; 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