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HAL (Smith and Kitzman 2023)

Configuration of HAL: Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 46.2.

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Evaluations and results

6 evaluations · 12 results. Different protocols are not a single leaderboard.

Sorted by Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants)	Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants)
HAL (Smith and Kitzman 2023)Evaluation	BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.909 (best in column)	0.909 (best in column)
HAL (Smith and Kitzman 2023)Evaluation	POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.75	0.75
HAL (Smith and Kitzman 2023)Evaluation	MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.673	0.673
HAL (Smith and Kitzman 2023)Evaluation	WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.24	0.24
HAL (Smith and Kitzman 2023)Evaluation	MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.165	0.165
HAL (Smith and Kitzman 2023)Evaluation	FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.148	0.148

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HAL (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)	0.909 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 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 B2; row HAL, column BRCA1
Configuration: HAL (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)	0.909 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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 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 B10; row Exon_HAL, column BRCA1
Configuration: HAL (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)	0.148 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 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 C2; row HAL, column FAS
Configuration: HAL (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)	0.148 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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 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 C10; row Exon_HAL, column FAS
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 (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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: 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 (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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: HAL (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)	0.75 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 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 E2; row HAL, column POU1F1
Configuration: HAL (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)	0.75 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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 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 E10; row Exon_HAL, column POU1F1
Configuration: HAL (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)	0.24 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) 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 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 G2; row HAL, column WT1
Configuration: HAL (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)	0.24 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) 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 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 G10; row Exon_HAL, 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-hal

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: HAL (Smith and Kitzman 2023)
foundation model eligible: false
missing metadata: version: reason: unreported; note: Version not printed; run through the web interface with wild-type PSI 90% (POU1F1), 50% (FAS), 60% (MST1R), 80% (BRCA1), 60% (WT1), 90% (MLH1)
parameters: Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 46.2 (Table S2 'Thresholds' column C)
source locator: Methods 'Scoring with eight splice effect predictors'; Additional file 3 'Thresholds'
limitations: HAL scores exonic variants only: 56.5% of the background set was unscored, so its threshold comes from exonic background variants, and its all-variant sensitivity equals its exonic sensitivity.
provenance note: HAL (Smith and Kitzman 2023) as run in the cited comparison.

Related records

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

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