Protocol

ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3)

Binary classification of assay-measured splice alteration by splice prediction tools.

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11 recorded evaluations, 121 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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11 evaluations · 121 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: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	56% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'Accuracy (%)'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	29 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'FN'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	2 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'FP'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0.16 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'MCC'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0 Count (variants without a score) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'Missing values'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	15% Negative predictive value percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'NPV (%)'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	95% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'PPV (%)'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	55% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'Sensitivity (%)'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	71% Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'Specificity (%)'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	5 True negatives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'TN'
Configuration: Alamut Consensus 3/4 (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	35 True positives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'Alamut Consensus 3/4', column 'TP'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	62% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'Accuracy (%)'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	24 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'FN'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	3 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'FP'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0.12 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'MCC'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	0 Count (variants without a score) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'Missing values'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	14% Negative predictive value percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'NPV (%)'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	93% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'PPV (%)'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	63% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'Sensitivity (%)'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	57% Specificity percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'Specificity (%)'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	4 True negatives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'TN'
Configuration: CADD (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	40 True positives count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CADD on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'CADD', column 'TP'
Configuration: DSSP (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	79% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DSSP on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'DSSP', column 'Accuracy (%)'
Configuration: DSSP (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	13 False negatives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DSSP on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'DSSP', column 'FN'
Configuration: DSSP (Riepe et al. 2021)	Protocol: ABCA4 noncanonical splice-site variants: classification against mini- or midigene splicing results (Riepe et al. Table 3) Dataset: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)	2 False positives count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DSSP on ABCA4 noncanonical splice-site variants splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss Aggregation: Not reported Benchmarking deep learning splice prediction tools using functional splice assays · Table 3 row 'DSSP', column 'FP'

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Benchmarking deep learning splice prediction tools using functional splice assays · Original source · Human Mutation 42(7):799, published online 2021-05-20; PMC8360004 full-text XML

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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss

areas: dna-genomes
contexts: research
protocol: Score each variant with each tool (missing Alamut scores set to zero); classify at a per-data-set cutoff and report the confusion matrix, accuracy, PPV, sensitivity, specificity, NPV and MCC (formulas in Table S2 of the article).
version: Table 3
source locator: Table 3; Methods 'Classification metrics and receiver operator curve'
limitations: Variants were selected for testing with Alamut tools (ABCA4) or MaxEntScan (MYBPC3), which can favour those tools and their relatives.; Cutoffs appear to be tuned on the same data set (Table 2 ROC-optimal thresholds); Tables 3-5 do not state the cutoff, so values may be optimistic.; Small single-gene sets with strong class imbalance (ABCA4 NCSS 90% positive, ABCA4 DI 26% positive).; Variants are from patients but splicing was measured in mini- or midigene assays in HEK293T, not in patient tissue.; The authors note the selection bias but report the opposite of what it would predict: Alamut 3/4 performs best on MYBPC3 and MaxEntScan only relatively well on ABCA4 (Discussion).; Spidex's unscored variants (5 in ABCA4 NCSS, 3 in MYBPC3) are counted in its confusion matrix without a stated class; MMSplice and Spidex are absent from the deep-intronic table because they scored fewer than half of those variants.
missing metadata: metric implementation: reason: unreported; note: Cutoff applied in Tables 3-5 is not stated; analysis scripts are at github.com/cmbi/Benchmarking_splice_prediction_tools (not read)

Related records

uses data: ABCA4 noncanonical splice-site variants (Riepe et al. benchmark set)
subject: selection_bias: splicing-follow-up-20261009-protocol-riepe2021-abca4-ncss
assessment: Alamut Consensus 3/4 on ABCA4 noncanonical splice-site variants
assessment: CADD on ABCA4 noncanonical splice-site variants
assessment: DSSP on ABCA4 noncanonical splice-site variants
assessment: GeneSplicer on ABCA4 noncanonical splice-site variants
assessment: MaxEntScan on ABCA4 noncanonical splice-site variants
assessment: MMSplice on ABCA4 noncanonical splice-site variants
assessment: NNSPLICE on ABCA4 noncanonical splice-site variants
assessment: Spidex on ABCA4 noncanonical splice-site variants
assessment: SpliceAI on ABCA4 noncanonical splice-site variants
assessment: SpliceRover on ABCA4 noncanonical splice-site variants
assessment: SpliceSiteFinder-like on ABCA4 noncanonical splice-site variants
assessed by: Prioritise variants for splicing experiments

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