PT  - JOURNAL ARTICLE
AU  - Lopez-Perolio, Irene
AU  - Leman, Raphaël
AU  - Behar, Raquel
AU  - Lattimore, Vanessa
AU  - Pearson, John F
AU  - Castéra, Laurent
AU  - Martins, Alexandra
AU  - Vaur, Dominique
AU  - Goardon, Nicolas
AU  - Davy, Grégoire
AU  - Garre, Pilar
AU  - García-Barberán, Vanesa
AU  - Llovet, Patricia
AU  - Pérez-Segura, Pedro
AU  - Díaz-Rubio, Eduardo
AU  - Caldés, Trinidad
AU  - Hruska, Kathleen S
AU  - Hsuan, Vickie
AU  - Wu, Sitao
AU  - Pesaran, Tina
AU  - Karam, Rachid
AU  - Vallon-Christersson, Johan
AU  - Borg, Ake
AU  - Investigators, kConFab
AU  - Valenzuela-Palomo, Alberto
AU  - Velasco, Eladio A
AU  - Southey, Melissa
AU  - Vreeswijk, Maaike P G
AU  - Devilee, Peter
AU  - Kvist, Anders
AU  - Spurdle, Amanda B
AU  - Walker, Logan C
AU  - Krieger, Sophie
AU  - de la Hoya, Miguel
TI  - Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report
AID  - 10.1136/jmedgenet-2018-105834
DP  - 2019 Jul 01
TA  - Journal of Medical Genetics
PG  - 453--460
VI  - 56
IP  - 7
4099  - http://jmg.bmj.com/content/56/7/453.short
4100  - http://jmg.bmj.com/content/56/7/453.full
SO  - J Med Genet2019 Jul 01; 56
AB  - 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.