Configuration

MMSplice (Smith and Kitzman 2023)

MMSplice (Smith and Kitzman 2023) as run in the cited comparison.

Overview

MMSplice (Smith and Kitzman 2023) as run in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

6 evaluations · 22 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.978 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 BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-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 B4; row MMSplice, column BRCA1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.818 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 BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-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 B12; row Exon_MMSplice, column BRCA1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.986 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 BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-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 B20; row Intron_MMSplice, column BRCA1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.969 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 BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-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 B28; row Intron_NonCanon_MMSplice, column BRCA1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.365 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 FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-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 C4; row MMSplice, column FAS
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.365 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 FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-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 C12; row Exon_MMSplice, column FAS
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: MMSplice (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0465 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 MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-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 F4; row MMSplice, column RON
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0337 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 MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-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 F12; row Exon_MMSplice, column RON
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0704 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 MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-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 F20; row Intron_MMSplice, column RON
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0758 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 MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-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 F28; row Intron_NonCanon_MMSplice, column RON
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.411 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 POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-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 E4; row MMSplice, column POU1F1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.357 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 POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-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 E12; row Exon_MMSplice, column POU1F1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.56 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 POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-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 E20; row Intron_MMSplice, column POU1F1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.421 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 POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-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 E28; row Intron_NonCanon_MMSplice, column POU1F1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.719 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 WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-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 G4; row MMSplice, column WT1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.4 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 WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-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 G12; row Exon_MMSplice, column WT1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.969 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 WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-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 G20; row Intron_MMSplice, column WT1
Configuration: MMSplice (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.95 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 WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-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 G28; row Intron_NonCanon_MMSplice, column WT1

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

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 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

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-10-6e93f504adfc · 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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-config-smith2023-mmsplice-2-2-0

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: MMSplice (Smith and Kitzman 2023)
foundation model eligible: false
version: 2.2.0
parameters: Default settings; delta logit PSI. Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 0.388854368912194 (Table S2 'Thresholds' column C)
source locator: Methods 'Scoring with eight splice effect predictors'; Additional file 3 'Thresholds'

Related records

configuration of: MMSplice
system: MMSplice on BRCA1 saturation genome editing, synonymous and intronic SNVs
system: MMSplice on FAS exon 6 saturation MPSA
system: MMSplice on MLH1 curated clinical splicing variants
system: MMSplice on MST1R (RON) exon 11 saturation MPSA
system: MMSplice on POU1F1 exon 2 saturation MPSA
system: MMSplice on WT1 exon 9 saturation MPSA

Suggest a correction