rs587780257

chr17-58696863-A-Gchr17-58696863-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5 BP4

The NM_058216.3(RAD51C):c.571+4A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000089 (0 hom.)
• Consequence: RAD51C NM_058216.3 splice_donor_region, intron
• Scores: Splicing: ADA: 0.1942
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:8
• Conservation: PhyloP100: 0.983

Genes affected

RAD51C (HGNC:9820): (RAD51 paralog C) This gene is a member of the RAD51 family. RAD51 family members are highly similar to bacterial RecA and Saccharomyces cerevisiae Rad51 and are known to be involved in the homologous recombination and repair of DNA. This protein can interact with other RAD51 paralogs and is reported to be important for Holliday junction resolution. Mutations in this gene are associated with Fanconi anemia-like syndrome. This gene is one of four localized to a region of chromosome 17q23 where amplification occurs frequently in breast tumors. Overexpression of the four genes during amplification has been observed and suggests a possible role in tumor progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PP5: Variant 17-58696863-A-G is Pathogenic according to our data. Variant chr17-58696863-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 128207.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Uncertain_significance=7, Pathogenic=1}. Variant chr17-58696863-A-G is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51C	NM_058216.3	c.571+4A>G		splice_donor_region_variant, intron_variant		ENST00000337432.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51C	ENST00000337432.9	c.571+4A>G		splice_donor_region_variant, intron_variant		1	NM_058216.3	P2

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152236 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000889 AC: 13 AN: 1461600 Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5 AN XY: 727128

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000108

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152236 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74384

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000655

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:8

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	University of Washington Department of Laboratory Medicine, University of Washington	Nov 20, 2015	This variant is predicted to alter a splice donor site. RT-PCR confirmed this variant causes exon 3 skipping. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 28, 2023	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 nucleotide position is well conserved in available vertebrate species. 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). In silico splice site analysis predicts that this alteration may weaken the native splice donor site. 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). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 11, 2023	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. -

Breast-ovarian cancer, familial, susceptibility to, 3 Pathogenic:1 Uncertain:1

Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 31, 2023	- -

Breast and/or ovarian cancer Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Jul 11, 2022

- -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Mendelics

Mar 30, 2022

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jul 31, 2023

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. -

Fanconi anemia complementation group O;C3150659:Breast-ovarian cancer, familial, susceptibility to, 3 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Counsyl

Aug 22, 2017

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jul 19, 2023

Targeted RNA analysis in a blood sample from an individual referred for testing at GeneDx demonstrated exon 3 skipping; however, this finding was also observed in controls. This result is consistent with RNA analysis published in Karam et al., 2019.; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Published functional studies are conflicting: some demonstrating a damaging effect due to skipping of exon 3 (Shirts et al., 2016; Dawson et al., 2019; Sanoguera-Miralles et al., 2020), one showing no aberrant splicing (Karam et al., 2019); This variant is associated with the following publications: (PMID: 17576681, 9536098, 26845104, 31642931, 33333735, 27535533, 35740625, 35728261, 32986223, 35264596, 31782267) -

RAD51C-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 26, 2024

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. -

Fanconi anemia complementation group O Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2024

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	17
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.19
dbscSNV1_RF	Benign	0.49
SpliceAI score (max)		0.38		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.24		Position offset: 0
DS_DL_spliceai		0.38		Position offset: -4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587780257; hg19: chr17-56774224;