A Japanese woman in her 50s underwent surgical resection for a tumor arising in the left retroperitoneum. Preoperative computed tomography (CT) and positron emission tomography (PET)-CT as well as intraoperative findings showed no distant metastasis, no obvious peritoneal dissemination, and no invasion of the uterus or ovaries (Supplementary Information). Histologically, the tumor was identified as a leiomyosarcoma of 12 cm × 11 cmin size. She was treated with postoperative chemotherapy with 6 cycles of doxorubicin, followed by chemotherapy with pazopanib for 8 months. During the observational follow-up period, imaging studies indicated peritoneal recurrence. While chemotherapy with pazopanib was promptly restarted, the tumor mass eventually grew to an obvious tumor in the peritoneum. She underwent debulking surgery twice for peritoneal tumors, but the tumors recurred. She received chemotherapy with gemcitabine and docetaxel, which was discontinued due to the onset of interstitial pneumonia. Cancer genome profiling was conducted to search for genome-matched treatment strategies in daily clinical practice in cancer precision medicine. She was referred to us for genetic counseling and interpretation of the RAD51D splicing variant, which was originally detected in the tumor genome profiling analysis. She had no family history of RAD51-related cancers or other types of malignancies, including sarcoma. In histological assessments, the tumor showed fascicular proliferation of spindle cells with eosinophilic cytoplasm. The nuclei showed moderate atypia, and some tumor cells had prominent nucleoli. Occasional mitotic figures were also observed. Tumor necrosis was not observed. In immunohistochemical studies performed at Mita Hospital adjunctive to the International University of Health and Welfare, Japan, the tumor cells were shown to be weakly positive for α-smooth muscle actin and desmin. These findings are consistent with a diagnosis of leiomyosarcoma, equivalent to histological grade 1 according to the French Federation of Cancer Centers Sarcoma Group (FNCLCC) grading system for sarcoma []. Through genomic profiling analysis of the designated 324 genes of the patient’s tumor samples by using the FoundationOne CDx® (Foundation Medicine Inc., MA, USA) oncology panel, two pathogenic variants in RAD51D (splicing variant) and TP53 (missense variant) and intermediate amplifications of four genes were detected. On the basis of the recommendations by the expert panel, which is a tumor board that provides molecular and clinical interpretations and suggestions for the results of oncology panel testing, the patient received genetic counseling and subsequently underwent germline analysis for RAD51D c.904-2A > T [NM_002878]. The same splicing variant of RAD51D was detected in the analysis of DNA extracted from lymphocytes by direct DNA sequencing using capillary gel electrophoresis and fluorescence detection (Sanger sequencing technique and application), which was performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. After extensive genetic counseling based on the results obtained from germline testing, her two daughters, shown as IV-1 and IV-2, also underwent predictive genetic testing, and both were found to be positive for the variant. To evaluate the potential effects of the spicing variant due to a single-nucleotide alteration at the 3′-end of intron 9, the schematic structure and location of which are shown in Fig. b, we used four computational prediction tools, Max Entropy Scan (MES), NetGene2, Splice Site Prediction by Neural Network (NNSplice), and Alternative Splice Site Predictor (ASSP) to analyze the potential effects of RAD51D c.904-2A > T [NM_002878]. All four tools predicted that the RAD51D variant attenuated normal splicing and yielded a shorter form of the RAD51D protein. Furthermore, cBROCA analysis, an experimental analysis for RNA as shown by Casadei et al. [], also predicted that this alteration would weaken the native splice acceptor site and create or strengthen alternative novel splice acceptor sites, resulting in shorter forms of the protein products of RAD51D. Taken together, these computational analyses suggest that a single-nucleotide alteration in intron 9 of RAD51D c.904-2A > T [NM_002878] attenuates normal splicing of RAD51D mRNA, resulting in the production of a shorter form of RAD51D protein (a representative truncated product is shown in Fig. c and d). Although there are no specific consensus domains in exon 10, which is truncated by attenuated splicing, the aggressively malignant phenotypes observed in this case would be evidence for RAD51D c.904-2A > T [NM_002878] as a novel loss-of-function variant involved in the formation and/or progression of malignant tumors. According to the ClinVar database (Variation ID: 472631) (, accessed in August 2021), the clinical significance of RAD51D c.904-2A > T [NM_002878] is likely pathogenic or uncertain, meaning that its clinical significance has not yet been determined and is a subject of debate in interpretation. Allele frequencies of RAD51D c.904-2A > T (NM_002878) in the general population were 6.60 × 10− 4 (ToMMo 8.3KJPN) and 4.13 × 10− 4 (HGVD ver2.3, dbSNP rsID: 1403784434) in Japanese people and 3.98 × 10− 6 in the global population, suggesting that the splicing variant RAD51D c.904-2A > T [NM_002878] was extremely rare in the global population as well as in Japan, which may be potentially indicate that it is a pathogenic variant.