Breast cancer is a common cancer in women around the world, and the incidence of breast cancer in women under the age of 50 is increasing recently. In addition, breast cancer is susceptible to hereditary factors, including family history, so it is important to identify and diagnose a patient's genetic variants. Therefore, this study aims to deepen our understanding of the genetic basis of breast cancer by identifying structural variants (SVs) induced by the Alu element in the BRCA1 gene. We utilized the high-throughput capabilities of the PacBio platform for long-read sequencing and Twist's target enrichment method to investigate Alu element-based SVs in the BRCA1 gene in 51 tissue samples (29 breast cancer tissues and 21 normal tissues) from Korean female breast cancer patients. Comprehensive analysis using SMRT Link software and third-party tools were used to uncover the presence and pattern of SVs. We identified a total of 55 large and small genetic pockmarks in the BRCA1 gene and interestingly, 41 of these events were caused by Alu elements. The insertion of LTR12C upstream of the BRCA1 gene was found to be common in cancerous tissues of 10 breast cancer patients and 5 normal tissues. By analyzing the impact of Alu element variants in the BRCA1 gene on the genetic causes of breast cancer, this study will contribute to the improvement of breast cancer diagnosis accuracy and the development of personalized treatment strategies. We expect that our results will play an important role in reducing mortality of breast cancer patients and provide new directions for breast cancer research.