Configuration

SPANR (Smith and Kitzman 2023)

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

Overview

SPANR (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.

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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: SPANR (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)	0.753 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 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 B6; row SPANR, column BRCA1
Configuration: SPANR (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)	0.273 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 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 B14; row Exon_SPANR, column BRCA1
Configuration: SPANR (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)	0.778 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 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 B22; row Intron_SPANR, column BRCA1
Configuration: SPANR (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)	0.583 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 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 B30; row Intron_NonCanon_SPANR, column BRCA1
Configuration: SPANR (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)	0.574 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 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 C6; row SPANR, column FAS
Configuration: SPANR (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)	0.574 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 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 C14; row Exon_SPANR, column FAS
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: 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: SPANR (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)	0.583 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 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 E6; row SPANR, column POU1F1
Configuration: SPANR (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)	0.514 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 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 E14; row Exon_SPANR, column POU1F1
Configuration: SPANR (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)	0.769 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 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 E22; row Intron_SPANR, column POU1F1
Configuration: SPANR (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)	0.7 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 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 E30; row Intron_NonCanon_SPANR, column POU1F1
Configuration: SPANR (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)	0.912 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 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 G6; row SPANR, column WT1
Configuration: SPANR (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)	0.96 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 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 G14; row Exon_SPANR, column WT1
Configuration: SPANR (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)	0.875 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 SPANR 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 G22; row Intron_SPANR, column WT1
Configuration: SPANR (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)	0.8 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 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 G30; row Intron_NonCanon_SPANR, column WT1

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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-config-smith2023-spanr-spidex

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: SPANR (Smith and Kitzman 2023)
foundation model eligible: false
missing metadata: version: reason: unreported; note: SPIDEX precomputed zdelta PSI scores; version not printed
parameters: Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 2.027 (Table S2 'Thresholds' column C)
source locator: Methods 'Scoring with eight splice effect predictors'; Additional file 3 'Thresholds'

Related records

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

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