Evidence claim

Relevance of WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) to "Prioritise variants for splicing experiments"

Use case: Prioritise variants for splicing experiments
Assessed by: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2)
Relevance: Proxy evidence
Endpoint: Sensitivity for WT1 exon 9 saturation MPSA splice-disruptive SNVs at thresholds calling 10% of 500,000 background SNVs, for HAL, S-Cap, MMSplice, SQUIRLS, SPANR, SpliceAI, Pangolin and ConSpliceML, overall and by variant class

Experimentally measured splicing of human SNVs, with several predictors scored on the same variants, informs which configurations to use when choosing SNVs for a follow-up splicing experiment. As for the existing MFASS mappings, transfer to a different assay, exon or follow-up capacity is not established.

8 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.

40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Citation locations 2 values source id splicing-follow-up-20261009-source-smith2023-table-s2 locator Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C source id splicing-follow-up-20261009-source-smith2023 locator Results 'Benchmarking in the context of genome-wide prediction'; Methods Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML Retrieved: 2026-10-09T20:49:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id splicing-follow-up-20261009-source-smith2023-table-s2 locator Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C source id splicing-follow-up-20261009-source-smith2023 locator Results 'Benchmarking in the context of genome-wide prediction'; Methods Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170 Retrieved: 2026-10-09T20:49:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `c5ed8dc1488f87a1aff766c0ed4c8b3faab148259ca6e6f28e729b9a57a700fa` Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). Inspected artifact
Comparison group smith2023-mpsa-tn10 Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML Retrieved: 2026-10-09T20:49:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group smith2023-mpsa-tn10 Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170 Retrieved: 2026-10-09T20:49:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `c5ed8dc1488f87a1aff766c0ed4c8b3faab148259ca6e6f28e729b9a57a700fa` Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). Inspected artifact
Comparison title Saturation splicing assays, sensitivity at a 10% genome-wide call rate (Smith and Kitzman 2023) Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML Retrieved: 2026-10-09T20:49:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Saturation splicing assays, sensitivity at a 10% genome-wide call rate (Smith and Kitzman 2023) Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170 Retrieved: 2026-10-09T20:49:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `c5ed8dc1488f87a1aff766c0ed4c8b3faab148259ca6e6f28e729b9a57a700fa` Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator and preserved conflicts before citing a result. Do not combine this mapping's evaluations with any other protocol's results, including the matched and historical MFASS protocols; populations, labels and thresholds differ. Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML Retrieved: 2026-10-09T20:49:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator and preserved conflicts before citing a result. Do not combine this mapping's evaluations with any other protocol's results, including the matched and historical MFASS protocols; populations, labels and thresholds differ. Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170 Retrieved: 2026-10-09T20:49:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `c5ed8dc1488f87a1aff766c0ed4c8b3faab148259ca6e6f28e729b9a57a700fa` Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). Inspected artifact
Endpoint Sensitivity for WT1 exon 9 saturation MPSA splice-disruptive SNVs at thresholds calling 10% of 500,000 background SNVs, for HAL, S-Cap, MMSplice, SQUIRLS, SPANR, SpliceAI, Pangolin and ConSpliceML, overall and by variant class Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML Retrieved: 2026-10-09T20:49:26Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Sensitivity for WT1 exon 9 saturation MPSA splice-disruptive SNVs at thresholds calling 10% of 500,000 background SNVs, for HAL, S-Cap, MMSplice, SQUIRLS, SPANR, SpliceAI, Pangolin and ConSpliceML, overall and by variant class Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170 Retrieved: 2026-10-09T20:49:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `c5ed8dc1488f87a1aff766c0ed4c8b3faab148259ca6e6f28e729b9a57a700fa` Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

2 source records and release history

Benchmarking splice variant prediction algorithms using massively parallel splicing assays · Original source · Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML
Smith and Kitzman 2023, Additional file 3 (Table S2) · Original source · 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-splicing-follow-up-20261009-smith2023-wt1-exon9-mpsa

field: links:assessed_by:splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10
value: splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10
relevance: proxy
endpoint: Sensitivity for WT1 exon 9 saturation MPSA splice-disruptive SNVs at thresholds calling 10% of 500,000 background SNVs, for HAL, S-Cap, MMSplice, SQUIRLS, SPANR, SpliceAI, Pangolin and ConSpliceML, overall and by variant class
rationale: Experimentally measured splicing of human SNVs, with several predictors scored on the same variants, informs which configurations to use when choosing SNVs for a follow-up splicing experiment. As for the existing MFASS mappings, transfer to a different assay, exon or follow-up capacity is not established.
constraints: Inspect every linked evaluation's source locator and preserved conflicts before citing a result.; Do not combine this mapping's evaluations with any other protocol's results, including the matched and historical MFASS protocols; populations, labels and thresholds differ.
limitations: Sensitivity only: the threshold fixes a genome-wide call rate, not specificity on the benchmark, so precision is not measured.; Per-dataset SDV and neutral counts are not printed in Table S2.; Blank cells (HAL intronic rows, FAS intronic columns) are not results and are not stored.; The masking setting behind Table S2 is not stated for SpliceAI or Pangolin; both masked and unmasked scores were computed.; HAL and S-Cap score only some variants, so their thresholds rest on part of the background; HAL's all-variant values equal its exonic values.; SpliceAI's threshold comes from version 1.3 precomputed background scores with unstated distance and masking; benchmark variants were scored with 1.3.1.
citation locators: source id: splicing-follow-up-20261009-source-smith2023-table-s2; locator: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; source id: splicing-follow-up-20261009-source-smith2023; locator: Results 'Benchmarking in the context of genome-wide prediction'; Methods
source locator: splicing-follow-up-20261009-source-smith2023-table-s2: Sheet 'Sensitivity 10% SDV', column 'WT1'; sheet 'Thresholds' column C; splicing-follow-up-20261009-source-smith2023: Results 'Benchmarking in the context of genome-wide prediction'; Methods
revision: 1
reason: Recorded from the splicing follow-up use-case pass 2026-10-09 (data/omics/use-case-coverage-splicing-follow-up-20261009/).
comparison group: smith2023-mpsa-tn10
comparison title: Saturation splicing assays, sensitivity at a 10% genome-wide call rate (Smith and Kitzman 2023)
headline metric: recall
stratum label: WT1 exon 9 saturation MPSA
stratum order: 5
reviewed evaluations: splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-conspliceml; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-hal; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-mmsplice-2-2-0; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-pangolin-1-0-2; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-s-cap; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-spanr-spidex; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-spliceai-1-3-1; splicing-follow-up-20261009-eval-smith2023-wt1-exon9-mpsa-squirls-1-0-0
review: method: automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; reviewed at: 2026-10-09T22:30:00Z; note: Independent review of endpoint fit, relevance grade, limitations and grouping against the use case and the source text; every value of the listed evaluations was checked against the pinned table. No execution, reproduction, human scientific review or clinical validation.
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subject: Prioritise variants for splicing experiments

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