Submissions for variant NM_058216.3(RAD51C):c.571+4A>G

gnomAD frequency: 0.00001  dbSNP: rs587780257

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000212940	SCV000150085	uncertain significance	not provided	2024-09-24	criteria provided, single submitter	clinical testing	Non-canonical splice variant demonstrated to result in skipping of exon 3, also observed in controls (PMID: 26845104, 31782267, 33333735, 31642931; GeneDx internal data); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 17576681, 9536098, 26845104, 31642931, 33333735, 35740625, 35728261, 32986223, 35264596, 31782267, 34326862, 35534704, 33606809)
Ambry Genetics	RCV000116176	SCV000185236	uncertain significance	Hereditary cancer-predisposing syndrome	2024-05-03	criteria provided, single submitter	clinical testing	The c.571+4A>G intronic variant results from an A to G substitution 4 nucleotides after coding exon 3 in the RAD51C gene. This alteration has been reported in individuals with breast and ovarian cancers, but it has also been identified in cancer free individuals (Shirts BH et al. Genet Med, 2016 10;18:974-81; Dawson LM et al. Mol Genet Genomic Med, 2020 02;8:e1070; Bandeira G et al. Breast Cancer, 2021 Mar;28:346-354; Guindalini RSC et al. Sci Rep, 2022 Mar;12:4190). Published RNA studies have identified skipping of exon 3 associated with this variant (Shirts BH et al. Genet Med, 2016 10;18:974-81; Dawson LM et al. Mol Genet Genomic Med, 2020 02;8:e1070; Sanoguera-Miralles L et al. Cancers (Basel), 2020 Dec;12). Internal RNA studies have demonstrated that this alteration results in a splice defect; however; the clinical impact of this abnormal splicing is unknown at this time (Ambry internal data). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice donor site. Based on the available evidence, the clinical significance of this variant remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000206409	SCV000261422	uncertain significance	Fanconi anemia complementation group O	2024-01-30	criteria provided, single submitter	clinical testing	This sequence change falls in intron 3 of the RAD51C gene. It does not directly change the encoded amino acid sequence of the RAD51C protein. It affects a nucleotide within the consensus splice site. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been observed in individual(s) with breast and/or ovarian cancer (PMID: 26845104, 31782267, 32986223, 34326862). ClinVar contains an entry for this variant (Variation ID: 128207). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with inconclusive levels of altered splicing (PMID: 26845104, 31782267; Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
University of Washington Department of Laboratory Medicine, University of Washington	RCV000116176	SCV000266229	uncertain significance	Hereditary cancer-predisposing syndrome	2015-11-20	criteria provided, single submitter	clinical testing	This variant is predicted to alter a splice donor site. RT-PCR confirmed this variant causes exon 3 skipping.
Color Diagnostics, LLC DBA Color Health	RCV000116176	SCV000691250	likely pathogenic	Hereditary cancer-predisposing syndrome	2023-12-11	criteria provided, single submitter	clinical testing	This variant causes an A to G nucleotide substitution at the +4 position of intron 3 of the RAD51C gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. RNA studies have shown that this variant leads to the skipping of exon 3 in studies using carrier-derived RNA or a mini-gene system (PMID: 26845104, 31782267, 33333735, 35740625). The aberrant transcript is predicted to create a premature translation stop signal and result in an absent or non-functional protein product. This variant has been reported in over 5 individuals affected with ovarian cancer (PMID: 31782267; Color internal data) and over 10 individuals affected with breast cancer (PMID: 26845104, 31782267, 32986223, 33606809, 35264596; Color internal data). This variant has been shown to segregate with breast and/or ovarian cancer, with reduced penetrance, in five multiplex families from the Newfoundland population that tested negative for variants in BRCA1, BRCA2, and other high and moderate cancer susceptibility genes (PMID: 31782267). A haplotype analysis has determined this variant to be a founder mutation in that population (PMID: 31782267). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of RAD51C function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.
Counsyl	RCV000662721	SCV000785476	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 3; Fanconi anemia complementation group O	2017-08-22	criteria provided, single submitter	clinical testing
Mendelics	RCV000709506	SCV000839330	pathogenic	Hereditary breast ovarian cancer syndrome	2022-03-30	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV001798364	SCV002043689	likely pathogenic	Breast and/or ovarian cancer	2022-07-11	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003323404	SCV004029807	uncertain significance	not specified	2023-07-31	criteria provided, single submitter	clinical testing	Variant summary: RAD51C c.571+4A>G alters a nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predict the variant abolishes a 5 splicing donor site. Three predict the variant weakens a 5' donor site. Three predict the variant creates a cryptic 5 donor site. At least two publications report experimental evidence that this variant affects mRNA splicing and causes exon 3 skipping (Dawson_2019, Sanoguera-Miralles_2022). However, one additional publication reports RNA studies demonstrate no abnormal splicing (Karam_2019). The variant allele was found at a frequency of 3.2e-05 in 31412 control chromosomes (gnomAD). c.571+4A>G has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome and other types of cancer as well as in healthy individuals (Shirts_2016, Karam_2019, Dawson_2019, Bandeira_2020, Guindalini_2022). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least one paper reports protein expression was significantly reduced in this variant heterozygote compared with a wild-type relative (Dawson_2019). The following publications have been ascertained in the context of this evaluation (PMID: 32986223, 31782267, 31642931, 33333735, 35740625, 26845104, 35264596). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified this variant as uncertain significance (n=6), likely pathogenic (n=2) and pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Baylor Genetics	RCV001356484	SCV004207955	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 3	2024-03-22	criteria provided, single submitter	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001356484	SCV001551668	uncertain significance	Breast-ovarian cancer, familial, susceptibility to, 3		no assertion criteria provided	clinical testing	The RAD51C c.571+4A>G variant was identified in 1 of 2904 proband chromosomes (frequency: 0.0003) from individuals or families referred for breast or colon multigene panel testing (Shirts 2016). The variant was also identified in dbSNP (ID: rs587780257) as “With other allele” and ClinVar (classified as uncertain significance by GeneDx, Invitae, University of Washington Dept. of Laboratory Medicine, Color Genomics Inc and Counsyl; and classified as likely benign by Ambry Genetics). The variant was not identified in Cosmic, MutDB, or LOVD 3.0 databases. The variant was identified in control databases in 1 of 30988 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European Non-Finnish in 1 of 15018 chromosomes (freq: 0.00007), while it was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, or South Asian populations. The c.571+4A>G variant is located in the 5' splice region but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. A study using RT-PCR showed that the RAD51C c.571+4A>G variant caused exon 3 skipping. In addition, 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.
PreventionGenetics, part of Exact Sciences	RCV004529956	SCV004727033	uncertain significance	RAD51C-related disorder	2024-01-26	no assertion criteria provided	clinical testing	The RAD51C c.571+4A>G variant is predicted to interfere with splicing. This variant has been reported in individuals with breast and/or ovarian cancer (Dawson et al. 2020. PubMed ID: 31782267; Bandeira et al. 2020. PubMed ID: 32986223; Shirts et al. 2016. PubMed ID: 26845104). In vitro experimental studies suggested this variant cause abnormal splicing (Dawson et al. 2020. PubMed ID: 31782267; Sanoguera-Miralles et al. 2020. PubMed ID: 33333735; Shirts et al. 2016. PubMed ID: 26845104) and reduced protein expression (Dawson et al. 2020. PubMed ID: 31782267). However, one additional RNA study reported this variant has no effect on splicing (Karam et al. 2019. PubMed ID: 31642931). This variant has been reported to segregate with breast and ovarian cancer in 5 families (Dawson et al. 2020. PubMed ID: 31782267). This variant is reported in 0.0065% of alleles in individuals of European (non-Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from uncertain to pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/128207/). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.