ArticleBioinformatics (Oxford, England)2023
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Article
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Investigating the contribution of rare non-coding variants in BRCA1, BRCA2 and PALB2 to hereditary breast cancer.NPJ breast cancer · 2026Article
- Cancer genomic profiling predicts pathogenicity ofmedRxiv : the preprint server for health sciences · 2026Article
- A practical framework for predicting splicing single nucleotide variants in exome sequencing.NAR genomics and bioinformatics · 2025Article
- Point of Care Testing, Rapid Next Generation Sequencing and Artificial Intelligence in Pediatric and Neonatal Healthcare: A Narrative Review.Pharmaceuticals (Basel, Switzerland) · 2025Review
- The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-inducedGenome research · 2025Article
- Decipher RNA isoform combinations from minigene splicing assays and massive parallel sequencing with MAGIC.Bioinformatics (Oxford, England) · 2025Article
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- Multi-tissue expression and splicing data prioritise anatomical subsite- and sex-specific colorectal cancer susceptibility genes.Nature communications · 2025Article
- Exploring the role of splicing in TP53 variant pathogenicity through predictions and minigene assays.Human genomics · 2025Article
- Estimation ofGenetics in medicine open · 2025Article
- Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes.Genome research · 2024Article
- An Update on Reported Variants in the Skeletal MuscleHuman mutation · 2024Review
- Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup.American journal of human genetics · 2023Article
- Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role forHGG advances · 2023Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
summarySpliceAI is a widely used splicing prediction tool and its most common application relies on the maximum delta score to assign variant impact on splicing. We developed the SpliceAI-10k calculator (SAI-10k-calc) to extend use of this tool to predict: the splicing aberration type including pseudoexonization, intron retention, partial exon deletion, and (multi)exon skipping using a 10 kb analysis window; the size of inserted or deleted sequence; the effect on reading frame; and the altered amino acid sequence. SAI-10k-calc has 95% sensitivity and 96% specificity for predicting variants that impact splicing, computed from a control dataset of 1212 single-nucleotide variants (SNVs) with curated splicing assay results. Notably, it has high performance (≥84% accuracy) for predicting pseudoexon and partial intron retention. The automated amino acid sequence prediction allows for efficient identification of variants that are expected to result in mRNA nonsense-mediated decay or translation of truncated proteins. AVAILABILITY AND IMPLEMENTATION: SAI-10k-calc is implemented in R (https://github.com/adavi4/SAI-10k-calc) and also available as a Microsoft Excel spreadsheet. Users can adjust the default thresholds to suit their target performance values.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.