Evidence claim
Evidence summary: splicing follow-up experiments
Summary of Prioritise variants for splicing experiments
Three independent comparisons score several splice predictors against experimentally measured splicing of human SNVs; none of their authors developed the tools compared. A fourth is reported by a tool's developers. Znabu et al. (2026, preprint) scored all 27,733 labelled MFASS reporter SNVs, of which 1,050 disrupt splicing. Average precision was 0.421 for Pangolin (bootstrap 95% interval 0.386 to 0.454), 0.321 for SpliceAI, 0.317 for SpliceTransformer, 0.256 for MMSplice and 0.228 for SPANR, with AUROC 0.888, 0.819, 0.786, 0.758 and 0.748. SpliceAI was given a score of zero where it returns none. This is a different MFASS population from the matched and v2 held-out protocols and is not pooled with them. Smith and Kitzman (2023) set each tool's threshold so that it flags 10% of 500,000 random exonic and near-exonic SNVs, then measured sensitivity on saturation assays, two of which their own group produced. SpliceAI detected 0.982 of splice-disruptive variants in BRCA1 saturation genome editing, 0.885 in POU1F1 exon 2, 0.860 in WT1 exon 9, 0.539 in FAS exon 6 and 0.237 in MST1R exon 11; Pangolin detected 0.982, 0.948, 0.667, 0.487 and 0.330. Sensitivity depends strongly on the exon, precision is not measured at these thresholds, and HAL and S-Cap score only part of the variants. A curated MLH1 column is recorded but judged outside scope, because its labels include patient RNA and a pathogenicity rule. Riepe et al. (2021) tested up to 11 tools on ABCA4 and MYBPC3 variants assayed in mini- or midigenes. MCC for SpliceAI was 0.42 for ABCA4 noncanonical splice sites, 0.84 for ABCA4 deep-intronic variants and 0.35 for MYBPC3, where the Alamut 3/4 consensus reached 0.53. Those variants were chosen for testing with Alamut or MaxEntScan, and the cutoffs were tuned on the same data. Jaganathan et al. (2026, preprint), the SpliceAI2 developers at Illumina, report Spearman correlation between predicted and measured exon-inclusion change for 283,121 single-nucleotide substitutions in 599 exons of the OpenSplice reporter assay: 0.59 for SpliceAI2, 0.55 for SpliceAI, 0.53 for Pangolin and 0.49 for AlphaGenome (Extended Data Fig. 2). The comparator scores are those released with OpenSplice, while SpliceAI2 was scored by its developers, and a rank correlation over all substitutions is not precision among variants chosen for an experiment. None of these sources measures how many variants a tool would select for a new experiment and how many of those then prove splice-disruptive, so all are proxy evidence for that choice. All values are transcribed from the publications, not reproduced. Reporter and minigene endpoints do not establish patient-RNA effects or pathogenicity, and results from different sources must not be pooled. This summary describes evidence and does not recommend a method.
Plain-language summary of what the reviewed evidence shows. Draft until reviewed.
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.
35 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field summary Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Claimed field summary Context-only references | Benchmarking deep learning splice prediction tools using functional splice assays splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Benchmarking splice variant prediction algorithms using massively parallel splicing assays splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Smith and Kitzman 2023, Additional file 3 (Table S2) splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). |
| Claimed field summary Context-only references | A Reproducible MFASS Benchmark of Splice-Disruption Predictors Reveals a Shared Exon-Interior Blind Spot splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.21.739871 v1, posted 2026-07-26; full-text PDF | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the PDF as served. The PDF ModDate is 2026-10-09 21:52:24 BST; a re-download at review on 2026-10-09 returned identical bytes. bioRxiv can re-stamp the PDF on later downloads, so if the hash stops matching, compare the text layer. |
Pinned records638 values
| A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
Pinned records638 values
| Benchmarking deep learning splice prediction tools using functional splice assays splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records638 values
| Benchmarking splice variant prediction algorithms using massively parallel splicing assays splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records638 values
| Smith and Kitzman 2023, Additional file 3 (Table S2) splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the MOESM3 xlsx member (zip SHA-256 e06758da73eda5d4ba9c61361514ed2d84573bf50df5bf8036102389e019d525; Europe PMC assembles the zip per request). |
Pinned records638 values
| A Reproducible MFASS Benchmark of Splice-Disruption Predictors Reveals a Shared Exon-Interior Blind Spot splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.21.739871 v1, posted 2026-07-26; full-text PDF | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of the PDF as served. The PDF ModDate is 2026-10-09 21:52:24 BST; a re-download at review on 2026-10-09 returned identical bytes. bioRxiv can re-stamp the PDF on later downloads, so if the hash stops matching, compare the text layer. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
5 source records and release history
- A Reproducible MFASS Benchmark of Splice-Disruption Predictors Reveals a Shared Exon-Interior Blind Spot · Original source · bioRxiv 2026.07.21.739871 v1, posted 2026-07-26; full-text PDF
- 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
- Benchmarking deep learning splice prediction tools using functional splice assays · Original source · Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML
- A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)
Technical metadata and extraction receipts
Stable ID: use-case-summary-splicing-follow-up
- field
- summary
- value
- Three independent comparisons score several splice predictors against experimentally measured splicing of human SNVs; none of their authors developed the tools compared. A fourth is reported by a tool's developers. Znabu et al. (2026, preprint) scored all 27,733 labelled MFASS reporter SNVs, of which 1,050 disrupt splicing. Average precision was 0.421 for Pangolin (bootstrap 95% interval 0.386 to 0.454), 0.321 for SpliceAI, 0.317 for SpliceTransformer, 0.256 for MMSplice and 0.228 for SPANR, with AUROC 0.888, 0.819, 0.786, 0.758 and 0.748. SpliceAI was given a score of zero where it returns none. This is a different MFASS population from the matched and v2 held-out protocols and is not pooled with them. Smith and Kitzman (2023) set each tool's threshold so that it flags 10% of 500,000 random exonic and near-exonic SNVs, then measured sensitivity on saturation assays, two of which their own group produced. SpliceAI detected 0.982 of splice-disruptive variants in BRCA1 saturation genome editing, 0.885 in POU1F1 exon 2, 0.860 in WT1 exon 9, 0.539 in FAS exon 6 and 0.237 in MST1R exon 11; Pangolin detected 0.982, 0.948, 0.667, 0.487 and 0.330. Sensitivity depends strongly on the exon, precision is not measured at these thresholds, and HAL and S-Cap score only part of the variants. A curated MLH1 column is recorded but judged outside scope, because its labels include patient RNA and a pathogenicity rule. Riepe et al. (2021) tested up to 11 tools on ABCA4 and MYBPC3 variants assayed in mini- or midigenes. MCC for SpliceAI was 0.42 for ABCA4 noncanonical splice sites, 0.84 for ABCA4 deep-intronic variants and 0.35 for MYBPC3, where the Alamut 3/4 consensus reached 0.53. Those variants were chosen for testing with Alamut or MaxEntScan, and the cutoffs were tuned on the same data. Jaganathan et al. (2026, preprint), the SpliceAI2 developers at Illumina, report Spearman correlation between predicted and measured exon-inclusion change for 283,121 single-nucleotide substitutions in 599 exons of the OpenSplice reporter assay: 0.59 for SpliceAI2, 0.55 for SpliceAI, 0.53 for Pangolin and 0.49 for AlphaGenome (Extended Data Fig. 2). The comparator scores are those released with OpenSplice, while SpliceAI2 was scored by its developers, and a rank correlation over all substitutions is not precision among variants chosen for an experiment. None of these sources measures how many variants a tool would select for a new experiment and how many of those then prove splice-disruptive, so all are proxy evidence for that choice. All values are transcribed from the publications, not reproduced. Reporter and minigene endpoints do not establish patient-RNA effects or pathogenicity, and results from different sources must not be pooled. This summary describes evidence and does not recommend a method.
- source locator
- splicing-follow-up-20261009-source-znabu2026: Section 4 results table; splicing-follow-up-20261009-source-smith2023-table-s2: Table S2, 10% call-rate sheet; splicing-follow-up-20261009-source-smith2023: Methods; splicing-follow-up-20261009-source-riepe2021: Tables 3 to 5; rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)', Methods 'Variant effect benchmarks'
- review
- method: independent-cell-check; scope-review; automated-source-review; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent reviewer of the SpliceAI2 batch; did not extract it; wrote the added sentences; no human review claimed; reviewed at: 2026-10-13T00:00:00Z; note: Adds the SpliceAI2 paper (Jaganathan et al. 2026, bioRxiv v1). Every added number traced to a source_checked result in data/omics/use-case-coverage-rna-splicing-20261013-spliceai2; earlier text unchanged. See docs/reviews/use-cases/spliceai2-2026-10-13.md. Previous review note: Drafted by the collector in coverage.json summary_proposal and corrected by the reviewer; every number traced to 25 stored source_checked results. Descriptive summary only; no execution, human scientific review or clinical validation. See docs/reviews/use-cases/splicing-follow-up-2026-10-09.md.
- pins
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