biostudies-literatureRowlands CCancer Research UKMedical Research CouncilNational Institute for Health Research (NIHR)Health Education EnglandWellcome Trust20607https://www.ebi.ac.uk/biostudies/studies/S-EPMC8523691biostudies-literatureUnknown11(1)The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individualsScientific reportsComparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders.PMC8523691MR/M009203/1MC_EX_MR/M009203/1MC_PC_14089RP-2016-07-011200990/Z/16/ZCL-2017-06-001HDR-9004Clayton-Smith JSergouniotis PSavage KTaylor Tavares ALGossan NWai HABevers RFowler TChan GCWilliams EPullinger JLopez FJEllingford JMHardcastle CMaleady-Crowe FArno GGenomics England Research ConsortiumBaralle DLahnstein LHubbard TJPWelland MJMinneci FStuckey AHirst RASieghart ACaulfield MJHamblin AMueller MThomas HBO'Donovan PO'Keefe RTAmbrose JCScott RHTucci AMoutsianas LBleda MLeigh SEAPatch CThomas ERABrittain HJones LJWebster ARDouglas AGLArumugam PJones EKasperaviciute DHenderson SPereira MBGomes-Silva BRogers TBoardman-Pretty FMcEntagart MRowlands CKayikci MRamsden SThompson SRMurugaesu NLeong IUSKousathanas ATanguy MSmith SCJackson RGiess ANewman WGRendon AWebb KSosinsky AO'Callaghan CPerez-Gil DNeed ACSawant KBlack GCMBoustred CRBeaman GSiddiq ACampbell COdhams CAWitkowsa KLord JRahim TWood SMfalseComparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders.The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals2021-01-01T00:00:00Z2021 Oct2026-07-14T14:36:14.144Z2024-11-08T11:39:18.202ZS-EPMC85236913466389110.1038/s41598-021-99747-2