Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: An ENIGMA report

Irene Lopez-Perolio, Raphaël Leman, Raquel Behar, Vanessa Lattimore, John F. Pearson, Laurent Castéra, Alexandra Martins, Dominique Vaur, Nicolas Goardon, Grégoire Davy, Pilar Garre, Vanesa García-Barberán, Patricia Llovet, Pedro Pérez-Segura, Eduardo Díaz-Rubio, Trinidad Caldés, Kathleen S. Hruska, Vickie Hsuan, Sitao Wu, Tina PesaranRachid Karam, Johan Vallon-Christersson, Ake Borg, kConFab Investigators, Alberto Valenzuela-Palomo, Eladio A. Velasco, Melissa Southey, Maaike P.G. Vreeswijk, Peter Devilee, Anders Kvist, Amanda B. Spurdle, Logan C. Walker, Sophie Krieger, Miguel De La Hoya

Research output: Contribution to journalArticleResearchpeer-review

10 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)453-460
Number of pages8
JournalJournal of Medical Genetics
Issue number7
Publication statusPublished - 1 Jul 2019
Externally publishedYes


  • acmg-Amp guidelines
  • palb2
  • pvs1
  • splicing
  • variant classification

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