FexSplice: A LightGBM-Based Model for Predicting the Splicing Effect of a Single Nucleotide Variant Affecting the First Nucleotide G of an Exon.

ABSTRACT: Single nucleotide variants (SNVs) affecting the first nucleotide G of an exon (Fex-SNVs) identified in various diseases are mostly recognized as missense or nonsense variants. Their effect on pre-mRNA splicing has been seldom analyzed, and no curated database is available. We previously reported that Fex-SNVs affect splicing when the length of the polypyrimidine tract is short or degenerate. However, we cannot readily predict the splicing effects of Fex-SNVs. We here scrutinized the available literature and identified 106 splicing-affecting Fex-SNVs based on experimental evidence. We similarly identified 106 neutral Fex-SNVs in the dbSNP database with a global minor allele frequency (MAF) of more than 0.01 and less than 0.50. We extracted 115 features representing the strength of splicing

SUBMITTER: Joudaki A 

PROVIDER: S-EPMC10531444 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature