Protocol

MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2)

Sensitivity for experimentally labelled splice-disruptive SNVs at tool thresholds matched on genome-wide call rate.

Overview

Sensitivity for experimentally labelled splice-disruptive SNVs at tool thresholds matched on genome-wide call rate.

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

8 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

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: 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)	0.262 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 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 F9; row ConSpliceML, column RON
Configuration: ConSpliceML (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)	0.292 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 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 F17; row Exon_ConSpliceML, column RON
Configuration: ConSpliceML (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)	0.204 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 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 F25; row Intron_ConSpliceML, column RON
Configuration: ConSpliceML (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)	0.144 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 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 F33; row Intron_NonCanon_ConSpliceML, column RON
Configuration: HAL (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)	0.165 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 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 F2; row HAL, column RON
Configuration: HAL (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)	0.165 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 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 F10; row Exon_HAL, 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)	0.0465 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: Pangolin (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)	0.33 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 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 F8; row Pangolin, column RON
Configuration: Pangolin (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)	0.352 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 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 F16; row Exon_Pangolin, column RON
Configuration: Pangolin (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)	0.289 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 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 F24; row Intron_Pangolin, column RON
Configuration: Pangolin (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)	0.235 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 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 F32; row Intron_NonCanon_Pangolin, column RON
Configuration: S-Cap (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)	0.133 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 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 F3; row S-Cap, column RON
Configuration: S-Cap (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)	0.116 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 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 F11; row Exon_S-Cap, column RON
Configuration: S-Cap (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)	0.142 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 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 F19; row Intron_S-Cap, column RON
Configuration: S-Cap (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)	0.0763 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 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 F27; row Intron_NonCanon_S-Cap, column RON
Configuration: SPANR (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)	0.103 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 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 F6; row SPANR, column RON
Configuration: SPANR (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)	0.105 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 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 F14; row Exon_SPANR, column RON
Configuration: SPANR (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)	0.0986 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 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 F22; row Intron_SPANR, column RON
Configuration: SPANR (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)	0.0303 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 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 F30; row Intron_NonCanon_SPANR, column RON
Configuration: SpliceAI (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)	0.237 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 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 F7; row SpliceAI, column RON
Configuration: SpliceAI (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)	0.24 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 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 F15; row Exon_SpliceAI, column RON
Configuration: SpliceAI (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)	0.232 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 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 F23; row Intron_SpliceAI, column RON

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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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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10

areas: dna-genomes
contexts: research
protocol: Label each benchmark variant splice-disruptive (SDV) or neutral as defined by its source study (intermediate variants removed). For each tool, take the score threshold at which it calls 10% of 500,000 random exonic and near-exonic background SNVs (MANE Select, internal coding exons +/- 100 bp) disruptive, and report sensitivity for benchmark SDVs at that threshold, overall and within exonic, intronic, and intronic-without-essential-splice-site variants.
version: Additional file 3 (Table S2) sheet 'Sensitivity 10% SDV'
source locator: Additional file 3 sheet 'Sensitivity 10% SDV', column 'RON'; Methods 'Statistical methods' and 'Random background variant set'
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.; Masking setting for SpliceAI and Pangolin in Table S2 is not stated.; HAL scores exonic variants only and S-Cap only some variants (56.5% and 61.0% of the background unscored), so their thresholds rest on part of the background, and HAL's all-variant values equal its exonic values.; SpliceAI benchmark scores are from 1.3.1, but its threshold comes from 1.3 precomputed background scores whose distance and masking settings are not stated.

Related records

uses data: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)
assessment: ConSpliceML on MST1R (RON) exon 11 saturation MPSA
assessment: HAL on MST1R (RON) exon 11 saturation MPSA
assessment: MMSplice on MST1R (RON) exon 11 saturation MPSA
assessment: Pangolin on MST1R (RON) exon 11 saturation MPSA
assessment: S-Cap on MST1R (RON) exon 11 saturation MPSA
assessment: SPANR on MST1R (RON) exon 11 saturation MPSA
assessment: SpliceAI on MST1R (RON) exon 11 saturation MPSA
assessment: SQUIRLS on MST1R (RON) exon 11 saturation MPSA
assessed by: Prioritise variants for splicing experiments

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