Configuration

SPiP 2.1 (Drost et al.)

SPiP as used by Drost et al.

Overview

SPiP as used by Drost et al.

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

Evaluations and results

3 evaluations · 24 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.906 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'CAGI6', cell I8; row SPiP, column AUPRC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.874 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'CAGI6', cell H8; row SPiP, column AUROC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.889 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell F21; row SPiP, column F1
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.762 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell H21; row SPiP, column Neg Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.914 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell G21; row SPiP, column Pos Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.914 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell E21; row SPiP, column Precision
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.865 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 SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell C21; row SPiP, column Sensitivity (Recall)
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, CAGI6 Splicing VUS subset (Drost et al. Data S1) Dataset: CAGI6 Splicing VUS variants as scored by Drost et al.	0.842 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 56 CAGI6 Splicing VUS variants rna-splicing-20261009-protocol-drost2025-cagi6 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'CAGI6 dataset', cell D21; row SPiP, column Specificity
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.89 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'In House', cell I13; row SPiP, column AUPRC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.817 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'In House', cell H13; row SPiP, column AUROC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.833 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F34; row SPiP, column F1
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.708 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H34; row SPiP, column Neg Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.843 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G34; row SPiP, column Pos Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.843 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E34; row SPiP, column Precision
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.822 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 SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C34; row SPiP, column Sensitivity (Recall)
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1) Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset	0.739 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on in-house scorable variants (count not printed) rna-splicing-20261009-protocol-drost2025-inhouse Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D34; row SPiP, column Specificity
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.889 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Entire Dataset', cell D11; row SPiP, column AUPRC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.83 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Entire Dataset', cell C11; row SPiP, column AUROC
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.846 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell F8; row SPiP, column F1
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.72 negative-predictive-value fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell H8; row SPiP, column Neg Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.86 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell G8; row SPiP, column Pos Pred Value
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.86 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell E8; row SPiP, column Precision
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.832 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 SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell C8; row SPiP, column Sensitivity (Recall)
Configuration: SPiP 2.1 (Drost et al.)	Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, all 243 scorable variants (Drost et al. Data S1) Dataset: Drost et al. RNA-tested clinical variants plus CAGI6 Splicing VUS, 243 scorable	0.761 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SPiP 2.1 on 243 scorable variants (in-house plus CAGI6) rna-splicing-20261009-protocol-drost2025-merged-243 Aggregation: Not reported Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'Entire Dataset', cell D8; row SPiP, column Specificity

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Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools · Original source · HGG Advances 7(1):100521, published online 2025-09-22; PMC12547740 full-text XML
Drost et al. 2025, Data S1 (Tables S1-S6) · Original source · mmc2.xlsx (Data S1. Tables S1-S6) inside the Europe PMC supplementaryFiles zip for PMC12547740

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261009-config-drost2025-spip

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: SPiP 2.1 (Drost et al.)
foundation model eligible: false
version: 2.1
parameters: Binary predictions at the literature threshold 0.452
source locator: Methods 'In silico splice predictions'; Results paragraph 3

Related records

configuration of: SPiP
system: SPiP 2.1 on 56 CAGI6 Splicing VUS variants
system: SPiP 2.1 on in-house scorable variants (count not printed)
system: SPiP 2.1 on 243 scorable variants (in-house plus CAGI6)

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