TY - JOUR T1 - Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report JF - Journal of Medical Genetics JO - J Med Genet SP - 453 LP - 460 DO - 10.1136/jmedgenet-2018-105834 VL - 56 IS - 7 AU - Irene Lopez-Perolio AU - Raphaël Leman AU - Raquel Behar AU - Vanessa Lattimore AU - John F Pearson AU - Laurent Castéra AU - Alexandra Martins AU - Dominique Vaur AU - Nicolas Goardon AU - Grégoire Davy AU - Pilar Garre AU - Vanesa García-Barberán AU - Patricia Llovet AU - Pedro Pérez-Segura AU - Eduardo Díaz-Rubio AU - Trinidad Caldés AU - Kathleen S Hruska AU - Vickie Hsuan AU - Sitao Wu AU - Tina Pesaran AU - Rachid Karam AU - Johan Vallon-Christersson AU - Ake Borg AU - kConFab Investigators AU - Alberto Valenzuela-Palomo AU - Eladio A Velasco AU - Melissa Southey AU - Maaike P G Vreeswijk AU - Peter Devilee AU - Anders Kvist AU - Amanda B Spurdle AU - Logan C Walker AU - Sophie Krieger AU - Miguel de la Hoya Y1 - 2019/07/01 UR - http://jmg.bmj.com/content/56/7/453.abstract N2 - Background PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2—without incurring overprediction—is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines.Methods Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212–1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant.Results We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies.Conclusions PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar. ER -