ArticleHuman mutation2022
SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing.
Article in Human mutation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
71 citing papers in PubMed, 91 citations in OpenAlex.
- Deep intronic ANK1 variants causing pseudo-exon inclusion in hereditary spherocytosis: Whole-genome sequencing and functional assessment.British journal of haematology · 2026Article
- Analysis of structure and conservation for supporting functional evaluation of PMS2 missense variants.European journal of human genetics : EJHG · 2026Article
- Results of a multigene panel testing approach targeting patients with suspected genetic predisposition to pancreatic ductal adenocarcinoma.European journal of human genetics : EJHG · 2026Article
- Article
- Article
- Decoding splicing variants in high-throughput sequencing: a functional validation approach integrating deep learning tools.European journal of human genetics : EJHG · 2026Article
- Reclassification of a BRCA2 variant, c.8487G > A (p.Gln2829Gln) located at 3' end of exon 19, from uncertain significance to likely pathogenic based on splicing alteration: a case report.Japanese journal of clinical oncology · 2026Article
- Clinical and genetic characteristics of a large cohort of children with Alagille syndrome: identification of 57 new variants in the JAG1 gene.Journal of human genetics · 2026Article
- 'Missing' disease-causing variants in Alport syndrome.Nature reviews. Nephrology · 2026Review
- Predicting human mRNA isoform levels from site-specific splicing kineticsbioRxiv : the preprint server for biology · 2026Article
- Expanding the Phenotypic Spectrum Associated With Loss-of-Function SMARCA4 Variants to Eye Developmental Anomalies.Clinical genetics · 2026Article
- Recurrent nonsense p.Trp3416* variant in theJournal of neuromuscular diseases · 2026Article
- A novel JK-null allele due to splicing variant.Transfusion · 2026Article
- Identification of the novel c.149-8C>G splicing variant in RHCE*02 that weakens C antigen expression.Transfusion · 2026Article
- Resolving non‑coding splice‑altering variants using an integrative genomic and transcriptomic workflow: application to FOXP1.Human genomics · 2026Article
- Identification of BCL2L11 as a Candidate Gene for Hereditary Predisposition to Non-Medullary Thyroid Cancer Using Familial Whole-Exome-Sequencing.Clinical genetics · 2026Article
- De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders.Nature communications · 2026Article
- Expanding the Recessive Spectrum of Dilated Cardiomyopathy: RNA-Level Validation of a HomozygousHuman mutation · 2026Article
- Article
- Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes.BMC genomics · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
36 authors at 9 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modeling splicing is essential for tackling the challenge of variant interpretation as each nucleotide variation can be pathogenic by affecting pre-mRNA splicing via disruption/creation of splicing motifs such as 5'/3' splice sites, branch sites, or splicing regulatory elements. Unfortunately, most in silico tools focus on a specific type of splicing motif, which is why we developed the Splicing Prediction Pipeline (SPiP) to perform, in one single bioinformatic analysis based on a machine learning approach, a comprehensive assessment of the variant effect on different splicing motifs. We gathered a curated set of 4616 variants scattered all along the sequence of 227 genes, with their corresponding splicing studies. The Bayesian analysis provided us with the number of control variants, that is, variants without impact on splicing, to mimic the deluge of variants from high-throughput sequencing data. Results show that SPiP can deal with the diversity of splicing alterations, with 83.13% sensitivity and 99% specificity to detect spliceogenic variants. Overall performance as measured by area under the receiving operator curve was 0.986, better than SpliceAI and SQUIRLS (0.965 and 0.766) for the same data set. SPiP lends itself to a unique suite for comprehensive prediction of spliceogenicity in the genomic medicine era. SPiP is available at: https://sourceforge.net/projects/splicing-prediction-pipeline/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.