Article
Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms
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- (1) Hospital Clínico San Carlos, grid.411068.a
- (2) University of Rouen, grid.10400.35
- (3) Instituto de Investigación Sanitaria de Santiago, grid.488911.d
- (4) University of Otago, grid.29980.3a
- (5) Leiden University Medical Center, grid.10419.3d
- (6) University of Southampton, grid.5491.9
- (7) University of Santiago de Compostela, grid.11794.3a
- (8) QIMR Berghofer Medical Research Institute, grid.1049.c
- (9) Philipp University of Marburg, grid.10253.35
- (10) Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen DK-2100, Denmark
- (11) Peter MacCallum Cancer Center, University of Melbourne, Melbourne, VIC 3002, Australia
- (12) Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- (13) Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel 24105, Germany
- (14) University of Münster, grid.5949.1
- (15) Hannover Medical School, grid.10423.34
- (16) Universitätsklinikum Tübingen, grid.411544.1
- (17) National Institutes of Health, grid.94365.3d
- (18) NorthShore University HealthSystem, grid.240372.0
- (19) Institute Curie, grid.418596.7
- (20) Centre Franois Baclesse, grid.476192.f
- (21) Ambry Genetics (United States), grid.465138.d
- (22) Royal Devon and Exeter Hospital, grid.416118.b
- (23) University of Melbourne, grid.1008.9
- (24) Medical University of Vienna, grid.22937.3d
- (25) Christchurch Hospital, grid.414299.3
- (26) South Australia Pathology, grid.414733.6
- (27) University of Adelaide, grid.1010.0
- (28) National Institute of Arthritis and Musculoskeletal and Skin Diseases, grid.420086.8
- (29) London School of Hygiene & Tropical Medicine, grid.8991.9
- (30) Institute of Cancer Research, grid.18886.3f
- (31) Heidelberg University, grid.7700.0
- (32) German Cancer Research Center, grid.7497.d
- (33) Gentofte Hospital, grid.411646.0, Capital Region
- (34) Herlev Hospital, grid.411900.d, Capital Region
- (35) University of Copenhagen, grid.5254.6, KU
- (36) Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Denmark
- (37) Karolinska Institute, grid.4714.6
- (38) University Cancer Center Hamburg, grid.412315.0
- (39) Fondazione IRCCS Istituto Nazionale dei Tumori, grid.417893.0
- (40) Associazione Volontari Italiani Sangue (AVIS) comunale di Milano, Milano 20139, Italy
- (41) Mayo Clinic, grid.66875.3a
- (42) Cancer Council Victoria, grid.3263.4
- (43) University of Toronto, grid.17063.33
- (44) Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- (45) University of Cambridge, grid.5335.0
- (46) Cyprus Institute of Neurology and Genetics, grid.417705.0
- (47) Department of Oncological Sciences
- (48) University of Utah, grid.223827.e
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Description
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 × 10-8 Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of ≈70-80% truncating transcripts, and ≈20-30% of in-frame Δ9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.