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Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry

European Journal of Human Genetics volume 31, pages 512–520 (2023)Cite this article

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Abstract

Splice-site variants in cardiac genes may predispose carriers to potentially lethal arrhythmias. To investigate, we screened 1315 probands and first-degree relatives enrolled in the Canadian Hearts in Rhythm Organization (HiRO) registry. 10% (134/1315) of patients in the HiRO registry carry variants within 10 base-pairs of the intron-exon boundary with 78% (104/134) otherwise genotype negative. These 134 probands were carriers of 57 unique variants. For each variant, American College of Medical Genetics and Genomics (ACMG) classification was revisited based on consensus between nine in silico tools. Due in part to the in silico algorithms, seven variants were reclassified from the original report, with the majority (6/7) downgraded. Our analyses predicted 53% (30/57) of variants to be likely/pathogenic. For the 57 variants, an average of 9 tools were able to score variants within splice sites, while 6.5 tools responded for variants outside these sites. With likely/pathogenic classification considered a positive outcome, the ACMG classification was used to calculate sensitivity/specificity of each tool. Among these, Combined Annotation Dependent Depletion (CADD) had good sensitivity (93%) and the highest response rate (131/134, 98%), dbscSNV was also sensitive (97%), and SpliceAI was the most specific (64%) tool. Splice variants remain an important consideration in gene elusive inherited arrhythmia syndromes. Screening for intronic variants, even when restricted to the ±10 positions as performed here may improve genetic testing yield. We compare 9 freely available in silico tools and provide recommendations regarding their predictive capabilities. Moreover, we highlight several novel cardiomyopathy-associated variants which merit further study.

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Fig. 1: RNA splicing schematic.
Fig. 2: Work-flow of utilized in silico tools.
Fig. 3: Position of identified splice-site variants.
Fig. 4: Predictive capability of in silico tools.

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The data underlying this article are available within the text, appendices, and online supplementary material.

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Funding

This work was supported by the Faculty of Medicine Summer Student Research Program at the University of British Columbia provided to KR. ZL was funded by the Michael Smith Foundation for Health Research and the Cardiology Academic Practice Plan at the University of British Columbia. The study was supported by the Heart in Rhythm Organization (Dr. Krahn, Principal Investigator) that receives support from the Canadian Institute of Health Research (RN380020 – 406814).

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Authors and Affiliations

  1. Center for Cardiovascular Innovation, Division of Cardiology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada

    Kaveh Rayani, Brianna Davies, Matthew Cheung, Drake Comber, Andrew D. Krahn & Zachary W. M. Laksman

  2. Section of Cardiac Electrophysiology, Division of Cardiology, Department of Medicine, Western University, London, ON, Canada

    Jason D. Roberts

  3. Cardiovascular Genetics Center, Montreal Heart Institute, Montreal, QC, Canada

    Rafik Tadros, Julia Cadrin-Tourigny & Mario Talajic

  4. Department of Medicine, Universite de Montreal, Montreal, QC, Canada

    Rafik Tadros, Julia Cadrin-Tourigny & Mario Talajic

  5. Heart Institute, University of Ottawa, Ottawa, ON, Canada

    Martin S. Green & Wael Alqarawi

  6. Population Health Research Institute, Hamilton, ON, Canada

    Jeffrey S. Healey

  7. Department of Medicine, Queen’s University, Kingston, ON, Canada

    Christopher S. Simpson

  8. Children’s Heart Centre, BC Children’s Hospital, Vancouver, BC, Canada

    Shubhayan Sanatani

  9. Institut Universitaire de Cardiologie et Pneumologie de Quebec, Laval University, Quebec City, QC, Canada

    Christian Steinberg

  10. Division of Cardiology, QEII Health Sciences Center, Halifax, NS, Canada

    Ciorsti MacIntyre & Martin Gardner

  11. St Michael’s Hospital, University of Toronto, Toronto, ON, Canada

    Paul Angaran

  12. Libin Cardiovascular Institute, University of Calgary, Calgary, AB, Canada

    Henry Duff

  13. Division of Cardiology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada

    Robert Hamilton

  14. Division of Medical Genetics, Island Health, Victoria, BC, Canada

    Laura Arbour

  15. Royal Jubilee Hospital, Victoria, BC, Canada

    Richard Leather

  16. Section of Cardiology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada

    Colette Seifer

  17. Division of Pediatric Cardiology, CHU Sainte-Justine, Universite de Montreal, Montreal, QC, Canada

    Anne Fournier

  18. Division of Pediatric Cardiology, University of Alberta Stollery Children’s Hospital, Edmonton, AB, Canada

    Joseph Atallah

  19. Division of Cardiology, Department of Medicine, University of Alberta, Edmonton, AB, Canada

    Shane Kimber

  20. Heart Health Institute, Scarborough Health Network, Scarborough, ON, Canada

    Bhavanesh Makanjee

  21. Division of Cardiology, McGill University Health Centre, Montreal, QC, Canada

    Jacqueline Joza

  22. Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia

    Richard D. Bagnall

  23. Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia

    Richard D. Bagnall

Authors
  1. Kaveh Rayani
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  2. Brianna Davies
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  4. Drake Comber
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  15. Robert Hamilton
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  16. Laura Arbour
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  18. Colette Seifer
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  21. Shane Kimber
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  29. Andrew D. Krahn
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  30. Zachary W. M. Laksman
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Contributions

Experimental design: KR, BD, RDB, ADK, ZWML. Data acquisition: KR, BD. Data analysis and interpretation: KR, BD, RDB, ADK, ZWML. Manuscript preparation: KR, BD, MC, DC, RDB, ADK, ZWML. Manuscript editting: KR, BD, MC, DC, JDR, RT, MSG, JSH, CSS, SS, CS, CM, PA, HD, RH, LA, RL, CS, AF, JA, SK, BM, WA, JC-T, JJ, MG, MT, RDB, ADK, ZWML.

Corresponding author

Correspondence to Zachary W. M. Laksman.

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The authors declare no competing interests.

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This project was conducted in compliance with the protocols and principles laid down in the Declaration of Helsinki and approved in full by the Providence Health/University of British Columbia ethics board (REB number H20-00129).

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Rayani, K., Davies, B., Cheung, M. et al. Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry. Eur J Hum Genet 31, 512–520 (2023). https://doi.org/10.1038/s41431-022-01193-9

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