ClinVar Genomic variation as it relates to human health

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. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs145779113, gnomAD 0.04%). This variant has been observed in individual(s) with breast and ovarian cancer and/or clinical features of Fanconi anemia (PMID: 21597919, 29278735, 30093976). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 216805). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 33333735; internal data). For these reasons, this variant has been classified as Pathogenic.

The c.571+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 3 in the RAD51C gene. This alteration was reported in 1/273 Chinese women with familial breast cancer who previously tested BRCA1/2 negative and also reported in an individual affected with ovarian cancer (Pang Z et al. Breast Cancer Res. Treat., 2011 Oct;129:1019-20; Chan GHJ et al. Oncotarget, 2018 Jul;9:30649-30660). Additionally, this variant has been reported in conjunction with another variant in RAD51C in an individual diagnosed with clinical features of Fanconi anemia (Jacquinet A et al. Eur J Med Genet, 2018 May;61:257-261). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies in the literature have demonstrated that this alteration results in impaired splicing (Sanoguera-Miralles L et al. Cancers (Basel), 2020 Dec;12:). Internal RNA studies have demonstrated that this alteration results in an incomplete splice defect; the clinical impact of this abnormal splicing is unknown at this time (Ambry internal data). Based on the available evidence, the clinical significance of this variant remains unclear.

This variant causes a G>A nucleotide substitution at the +5 position of intron 3 of the RAD51C gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. A mini-gene splice assay has shown that this variant results in out-of-frame skipping of exon 3 in over 90% of the transcripts (PMID: 33333735). This variant is expected to result in an absent or non-functional protein product. This variant has been observed in an individual affected with ovarian cancer (PMID: 30093976), in two individuals affected with breast cancer (PMID: 21597919; Lertwilaiwittaya et al., 2020, DOI: https://doi.org/10.21203/rs.3.rs-122156/v1), and in an individual having clinical features of Fanconi anemia (PMID: 29278735, 36909564). All of these affected individuals were of East Asian ethnicity. This variant has been identified in 7/282860 chromosomes (7/19250 East Asian chromosomes) 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.

PM2_Supporting+PS3+PS4_Supporting

Variant summary: RAD51C c.571+5G>A alters a non-conserved 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: Three predict the variant weakens a 5' donor site. One predicts the variant abolishes a 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (example: Sanoguera-Miralles_2020). The variant allele was found at a frequency of 1.6e-05 in 251446 control chromosomes (gnomAD). c.571+5G>A has been reported in the literature in at least an individual affected with Fanconi Anemia as well as in individuals with breast and/or ovarian cancers (example: Jacquinet_2018, Pang_2011, Chan_2018, Yao_2022). The following publications have been ascertained in the context of this evaluation (PMID: 30093976, 29278735, 21597919, 33333735, 35186721). ClinVar contains an entry for this variant (Variation ID: 216805). Based on the evidence outlined above, the variant was classified as likely pathogenic.

The RAD51C c.571+5G>A variant has been reported in the published literature in individuals with breast cancer (PMID: 21597919 (2011)), ovarian cancer (PMID: 30093976 (2018)), and uterine and colorectal cancer (PMID: 34326862 (2021)). In addition, this variant has been reported to result in aberrant RAD51C splicing (PMID: 33333735 (2020)). The frequency of this variant in the general population, 0.00035 (7/19952 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper RAD51C mRNA splicing. Based on the available information, this variant is classified as likely pathogenic.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 35740625, 39299233]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 29278735].

PS3, PM2