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Reports on the benign variants of <jats:italic>BRCA<\/jats:italic> genes are limited. However, the definition of these variants might be altered with the accumulation of clinical evidence. Therefore, in the present study, we focused on benign single nucleotide polymorphisms (SNPs) of <jats:italic>BRCA<\/jats:italic> genes. Linkage disequilibrium was calculated from whole genome sequencing of the <jats:italic>BRCA<\/jats:italic> genes obtained from 500 healthy controls and 49 breast cancer patients. Sanger sequencing was used to confirm the mutation. The linkage disequilibrium was noted for seven and three SNPs in the <jats:italic>BRCA1<\/jats:italic> and <jats:italic>BRCA2<\/jats:italic> genes, respectively. Breast cancer with <jats:italic>BRCA1<\/jats:italic>\/<jats:italic>2<\/jats:italic> linkage disequilibrium was not correlated with a personal history of benign diseases or family history of cancer. Nevertheless, breast cancer with <jats:italic>BRCA1<\/jats:italic> linkage disequilibrium was correlated with high tumor\u2010infiltrating lymphocytes and positive extensive intraductal components. The patients with <jats:italic>BRCA1<\/jats:italic> linkage disequilibrium tended to have worse disease\u2010specific survival. Cancers with <jats:italic>BRCA2<\/jats:italic> linkage disequilibrium are associated with a lower ratio of grade III cancer. Moreover, patients with <jats:italic>BRCA2<\/jats:italic> linkage disequilibrium tended to have better overall survival. In conclusion, linkage disequilibrium from benign SNPs of the <jats:italic>BRCA<\/jats:italic> genes potentially affects cancer characteristics.<\/jats:p>","DOI":"10.1111\/cas.16364","type":"journal-article","created":{"date-parts":[[2024,10,12]],"date-time":"2024-10-12T10:15:27Z","timestamp":1728728127000},"page":"3973-3985","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Benign polymorphisms in the <scp><i>BRCA<\/i><\/scp> genes with linkage disequilibrium is associated with cancer characteristics"],"prefix":"10.1111","volume":"115","author":[{"given":"Kuo\u2010Ting","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Surgery National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University  Tainan Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dao\u2010Peng","family":"Chen","sequence":"additional","affiliation":[{"name":"Kim Forest Enterprise Co., Ltd.  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