The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity.

Dr. Jonine Figueroa, PhD
Dr. Jonine Figueroa, PhD
Usher Institute of Population Health Sciences and Informatics
Chancellor's Fellow
Molecular epidemiology
Edinburgh, Scotland | United Kingdom
Mara Colombo Irene Lòpez-Perolio Huong D Meeks Laura Caleca Michael T Parsons Hongyan Li Giovanna De Vecchi Emma Tudini Claudia Foglia Patrizia Mondini Siranoush Manoukian Raquel Behar Encarna B Gómez Garcia Alfons Meindl Marco Montagna Dieter Niederacher Ane Y Schmidt Liliana Varesco Barbara Wappenschmidt Manjeet K Bolla Joe Dennis Kyriaki Michailidou Qin Wang Kristiina Aittomäki Irene L Andrulis Hoda Anton-Culver Volker Arndt Matthias W Beckmann Alicia Beeghly-Fadel Javier Benitez Bram Boeckx Natalia V Bogdanova Stig E Bojesen Bernardo Bonanni Hiltrud Brauch Hermann Brenner Barbara Burwinkel Jenny Chang-Claude Don M Conroy Fergus J Couch Angela Cox Simon S Cross Kamila Czene Peter Devilee Thilo Dörk Mikael Eriksson Peter A Fasching Olivia Fletcher Henrik Flyger Marike Gabrielson Montserrat García-Closas Graham G Giles Anna González-Neira Pascal Guénel Christopher A Haiman Per Hall Ute Hamann Mikael Hartman Jan Hauke Antoinette Hollestelle John L Hopper Anna Jakubowska Audrey Jung Veli-Matti Kosma Diether Lambrechts Loid Le Marchand Annika Lindblom Jan Lubinski Arto Mannermaa Sara Margolin Hui Miao Roger L Milne Susan L Neuhausen Heli Nevanlinna Janet E Olson Paolo Peterlongo Julian Peto Katri Pylkäs Elinor J Sawyer Marjanka K Schmidt Rita K Schmutzler Andreas Schneeweiss Minouk J Schoemaker Mee Hoong See Melissa C Southey Anthony Swerdlow Soo H Teo Amanda E Toland Ian Tomlinson Thérèse Truong Christi J van Asperen Ans M W van den Ouweland Lizet E van der Kolk Robert Winqvist Drakoulis Yannoukakos Wei Zheng Alison M Dunning Douglas F Easton Alex Henderson Frans B L Hogervorst Louise Izatt Kenneth Offitt Lucy E Side Elizabeth J van Rensburg Study Embrace Study Hebon Lesley McGuffog Antonis C Antoniou Georgia Chenevix-Trench Amanda B Spurdle David E Goldgar Miguel de la Hoya Paolo Radice

Hum Mutat 2018 05 6;39(5):729-741. Epub 2018 Apr 6.

Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy.

Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10 . There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.

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May 2018
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