Dataset

MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)

296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive.

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Release 2026-10-10-6e93f504adfc · Evidence verified: Not verified

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Evaluation results

8 evaluations · 30 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ConSpliceML (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.931 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ConSpliceML on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D9; row ConSpliceML, column MLH1
Configuration: ConSpliceML (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.816 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ConSpliceML on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D17; row Exon_ConSpliceML, column MLH1
Configuration: ConSpliceML (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.982 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ConSpliceML on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D25; row Intron_ConSpliceML, column MLH1
Configuration: ConSpliceML (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.931 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ConSpliceML on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D33; row Intron_NonCanon_ConSpliceML, column MLH1
Configuration: HAL (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.673 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HAL on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D2; row HAL, column MLH1
Configuration: HAL (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.673 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HAL on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D10; row Exon_HAL, column MLH1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.875 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MMSplice on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D4; row MMSplice, column MLH1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.612 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MMSplice on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D12; row Exon_MMSplice, column MLH1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.991 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MMSplice on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D20; row Intron_MMSplice, column MLH1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source MMSplice on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D28; row Intron_NonCanon_MMSplice, column MLH1
Configuration: Pangolin (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.931 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pangolin on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D8; row Pangolin, column MLH1
Configuration: Pangolin (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.776 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pangolin on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D16; row Exon_Pangolin, column MLH1
Configuration: Pangolin (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pangolin on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D24; row Intron_Pangolin, column MLH1
Configuration: Pangolin (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Pangolin on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D32; row Intron_NonCanon_Pangolin, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.836 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D3; row S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D11; row Exon_S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.874 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D19; row Intron_S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.517 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D27; row Intron_NonCanon_S-Cap, column MLH1
Configuration: SPANR (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.752 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPANR on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D6; row SPANR, column MLH1
Configuration: SPANR (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.469 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPANR on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D14; row Exon_SPANR, column MLH1
Configuration: SPANR (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.88 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPANR on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D22; row Intron_SPANR, column MLH1
Configuration: SPANR (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.655 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPANR on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D30; row Intron_NonCanon_SPANR, column MLH1
Configuration: SpliceAI (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.931 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D7; row SpliceAI, column MLH1
Configuration: SpliceAI (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.776 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D15; row Exon_SpliceAI, column MLH1
Configuration: SpliceAI (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SpliceAI on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D23; row Intron_SpliceAI, column MLH1

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Dataset and evaluation context

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Evidence

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Evidence table

Inspect claims, sources and review details

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12 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
attributes.population 296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive. Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.population` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.population 296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive. Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.population` 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
attributes.source_locator Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.source_locator` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.source_locator` 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
attributes.split No split; whole set is the benchmark Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.split` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.split No split; whole set is the benchmark Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.split` 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
attributes.version Additional file 2 Table S1 (as published) Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.version` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.version Additional file 2 Table S1 (as published) Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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.version` 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
description 296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive. Context-only references	Benchmarking splice variant prediction algorithms using massively parallel splicing assays Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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: `description` Source artifact SHA-256: `5aceff067af63ab59400ade7dd7db563a16fc7f4d6db6fa55d5b34689f7a0769` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
description 296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive. Context-only references	Smith and Kitzman 2023, Additional file 3 (Table S2) Original source ↗ Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants' 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: `description` 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 2026-10-10-6e93f504adfc · Record review: source checked

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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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Stable ID: splicing-follow-up-20261009-data-smith2023-mlh1-curated

areas: dna-genomes
contexts: research
version: Additional file 2 Table S1 (as published)
split: No split; whole set is the benchmark
population: 296 MLH1 single-base substitutions curated from 77 publications, with splicing supported by patient blood RNA RT-PCR or minigene analysis; essential splice-site variants from Lynch syndrome patients included without molecular evidence; 160 splice-disruptive.
source locator: Results 'A validation set of variants and splice effects'; Methods 'Saturation mutagenesis datasets' and 'Manual curation of clinical MLH1 variants'
missing metadata: variants: reason: unextracted; note: Per-dataset counts are in Additional file 2 and Figure 1, not read

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