Rare sequence variants in the non-coding part of the BRCA genes are often reported as variants of uncertain significance (VUS), which leave patients and doctors in a challenging position. The aim of this study was to determine the pathogenicity of the BRCA1 c.5407-25T>A variant found in 20 families from Norway, France and United States with suspected hereditary breast and ovarian cancer. This was done by combining clinical and family information with allele frequency data, and assessment of the variant’s effect on mRNA splicing. Mean age at breast (n = 12) and ovarian (n = 11) cancer diagnosis in female carriers was 49.9 and 60.4 years, respectively. The mean Manchester score in the 20 families was 16.4. The allele frequency of BRCA1 c.5407-25T>A was 1/64,566 in non-Finnish Europeans (gnomAD database v2.1.1). We found the variant in 1/400 anonymous Norwegian blood donors and 0/784 in-house exomes. Sequencing of patient-derived cDNA from blood, normal breast and ovarian tissue showed that BRCA1 c.5407-25T>A leads to skipping of exon 23, resulting in frameshift and protein truncation: p.(Gly1803GlnfsTer11). Western blot analysis of transiently expressed BRCA1 proteins in HeLa cells showed a reduced amount of the truncated protein compared with wild type. Noteworthily, we found that a small amount of full-length transcript was also generated from the c.5407-25T>A allele, potentially explaining the intermediate cancer burden in families carrying this variant. In summary, our results show that BRCA1 c.5407-25T>A leads to partial skipping of exon 23, and could represent a likely pathogenic variant with reduced penetrance.

BRCA基因非编码部分的罕见序列变异通常被报告为不确定重要性（VUS）变异，这使患者和医生处于挑战性地位。这项研究的目的是确定BRCA1 c.5407-25T>变异株的致病性，该变异株在来自挪威，法国和美国的20个家庭中发现，患有怀疑的遗传性乳腺癌和卵巢癌。这是通过将临床和家族信息与等位基因频率数据相结合，并评估变体对mRNA剪接的影响来完成的。 女性携带者的乳腺癌平均年龄（n  = 12）和卵巢癌（n = 11）分别为49.9岁和60.4岁。在20个家庭中，曼彻斯特平均得分为16.4。的等位基因频率在非芬兰欧洲人中，BRCA1 c.5407-25T> A为1 / 64,566（gnomAD数据库v2.1.1）。我们在1/400个匿名挪威献血者和0/784个内部外显子组中发现了这种变异。对患者血液，正常乳腺和卵巢组织中的cDNA进行测序显示，BRCA1 c.5407-25T> A导致外显子23跳过，导致移码和蛋白截短：p。（Gly1803GlnfsTer11）。对HeLa细胞中瞬时表达的BRCA1蛋白进行的蛋白质印迹分析表明，与野生型相比，截短的蛋白减少了。值得注意的是，我们发现从c.5407-25T> A等位基因也产生了少量的全长转录本，这可能解释了携带该变异体的家庭中癌症的负担。总而言之，我们的结果表明BRCA1 c.5407-25T> A导致外显子23的部分跳过，可能代表着外显率降低的可能的致病变异。