17-58709857-A-G

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Strong PP3_Strong PP5_Very_Strong

The NM_058216.3(RAD51C):c.706-2A>G variant causes a splice acceptor change. The variant allele was found at a frequency of 0.0000299 in 1,602,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000031 (0 hom.)
• Consequence: RAD51C NM_058216.3 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:23
• Conservation: PhyloP100: 6.97

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 Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.1158267 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.2, offset of 10, new splice context is: ctgtatttgggttcgactAGtga. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 17-58709857-A-G is Pathogenic according to our data. Variant chr17-58709857-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 128209.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-58709857-A-G is described in Lovd as [Likely_pathogenic]. Variant chr17-58709857-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51C	NM_058216.3	c.706-2A>G		splice_acceptor_variant		ENST00000337432.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51C	ENST00000337432.9	c.706-2A>G		splice_acceptor_variant		1	NM_058216.3	P2

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 151984 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251368 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135850

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000440

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000310 AC: 45 AN: 1450912 Hom.: 0 Cov.: 30 AF XY: 0.0000374 AC XY: 27 AN XY: 722504

Gnomad4 AFR exome AF: 0.00

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: 0.0000187

Gnomad4 NFE exome AF: 0.0000381

Gnomad4 OTH exome AF: 0.0000333

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 151984 Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2 AN XY: 74218

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000593 Hom.: 0

ExAC AF: 0.0000247 AC: 3

EpiCase AF: 0.00

EpiControl AF: 0.000178

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:23

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 3 Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 22, 2023	- -
Pathogenic, criteria provided, single submitter	research	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Dec 09, 2022	PVS1, PS3, PS4_STR, PP1 -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 15, 2019	- -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The RAD51C c.706-2A>G variant was identified in 12 of 15014 proband chromosomes (frequency: 0.0008) from individuals or families with breast and ovarian cancer (Castera 2014, Couch 2015, Golmard 2013, Loveday 2012, Song 2015). The variant was also identified in the following databases: dbSNP (ID: rs587780259) as "With Pathogenic allele", ClinVar (5x pathogenic, 2x likely pathogenic), Clinvitae, and LOVD 3.0 (1x). The variant was not identified in Cosmic or the MutDB database. The variant was identified in control databases in 6 of 277092 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). It was observed in the European population in 6 of 126600 chromosomes (freq: 0.00005), but not in the African, Other, Latino, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. Functional studies utilizing mRNA from lymphoblastoid cell lines shows this variant affects splicing, resulting in in-frame skipping of exon 5 (Golmard 2013, Davy 2017). The c.706-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Apr 06, 2023	This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. -

not provided Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 22, 2023	Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant demonstrated to result in an in-frame loss of the adjacent exon (Sanoguera-Miralles et al., 2022) in a gene for which loss of function is a known mechanism of disease; Observed in individuals with breast and ovarian cancer (Walsh et al., 2011; Loveday et al., 2012; Golmard et al., 2013; Couch et al., 2015; Song et al., 2015; Golmard et al., 2017; Harter et al., 2017; Kotoula et al., 2017; Lilyquist et al., 2017; Koczkowska et al., 2018; Li et al., 2019; Bhai et al., 2021); This variant is associated with the following publications: (PMID: 25470109, 24240112, 28123851, 29053726, 29143133, 30949688, 24315737, 22006311, 22538716, 24139550, 24549055, 25452441, 26261251, 26681312, 26720728, 29255180, 28152038, 28776603, 28905878, 31173646, 30441849, 30322717, 31589614, 33333735, 29961768, 32107557, 32359370, 20400964, 22167183, 26354865, 21990120, 20400963, 35740625, 14704354, 34326862, 29922827, 28888541) -
Likely pathogenic, no assertion criteria provided	curation	Leiden Open Variation Database	Nov 02, 2014	Curator: Arleen D. Auerbach. Submitter to LOVD: Johan den Dunnen. -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	RAD51C: PVS1, PS3:Supporting, PS4:Supporting -

Fanconi anemia complementation group O Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 13, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 26, 2024	This sequence change affects an acceptor splice site in intron 4 of the RAD51C gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs587780259, gnomAD 0.005%). Disruption of this splice site has been observed in individual(s) with breast cancer and ovarian cancer (PMID: 22006311, 22538716, 24549055, 25452441, 26261251, 26681312, 29255180). ClinVar contains an entry for this variant (Variation ID: 128209). Studies have shown that disruption of this splice site results in skipping of exon 5, but is expected to preserve the integrity of the reading-frame (PMID: 22006311, 24139550; Invitae). This variant disrupts a region of the RAD51C protein in which other variant(s) (p.Arg258His) have been determined to be pathogenic (PMID: 20400963, 22167183, 26354865). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 22, 2021	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, no assertion criteria provided	research	Division of Human Genetics, Children's Hospital of Philadelphia	Aug 16, 2016	- -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 08, 2024	This variant causes an A to G nucleotide substitution at the -2 position of intron 4 of the RAD51C gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. RNA studies have shown that this variant causes the skipping of exon 5, resulting in an in-frame deletion of 44 amino acids including the Walker B motif in the ATP-binding domain of the RAD51C protein (PMID: 22006311, 24139550, 28905878, 33333735). This variant is expected to cause a defect in RAD51C protein function. This variant has been reported in many individuals affected with breast or ovarian cancer (PMID: 22006311, 22538716, 24139550, 25452441, 26261251, 26681312, 29053726, 29255180). This variant has been identified in 6/282746 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 Pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Jan 25, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 29, 2022	The c.706-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides upstream from coding exon 5 of the RAD51C gene. This alteration has been reported in multiple individuals with personal and/or family history of breast and/or ovarian cancer (Meindl A et al. Nat. Genet. 2010 May;42:410-4; Walsh T et al. Proc. Natl. Acad. Sci. USA. 2011 Nov;108:18032-7; Loveday C et al. Nat. Genet. 2012 May;44:475-6; Golmard L et al. BMC Cancer. 2013 Oct;13:484; Castéra L et al. Eur. J. Hum. Genet. 2014 Nov;22:1305-13; Song H et al. J. Clin. Oncol. 2015 Sep;33:2901-7; Couch FJ et al. J. Clin. Oncol. 2015 Feb;33:304-11; Susswein LR et al. Genet. Med. 2016 Aug;18(8):823-32; Kotoula V et al. Am J Cancer Res. 2017 Jan;7:98-114; Harter P et al. PLoS ONE. 2017 Oct;12:e0186043; Golmard L et al. Eur. J. Hum. Genet. 2017 12;25:1345-1353). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. RNA analyses have shown that this mutation leads to skipping of exon 5, resulting in an in-frame deletion of 44 amino acid residues including the Walker B box in the functionally important RecA domain (Walsh T et al. Proc. Natl. Acad. Sci. USA. 2011 Nov;108:18032-7; Golmard L et al. BMC Cancer. 2013 Oct;13:484; Davy G et al. Eur. J. Hum. Genet. 2017 10;25:1147-1154; Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Fanconi anemia complementation group O;C3150659:Breast-ovarian cancer, familial, susceptibility to, 3 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Jan 12, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -

Neoplasm of ovary Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Dec 01, 2018

- -

RAD51C-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 17, 2023

The RAD51C c.706-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant was reported in an individual with peritoneal carcinoma, an individual with squamous cell carcinoma of the head and neck, an individual with pancreatic cancer, individuals with breast and/or ovarian cancer, individuals undergoing hereditary cancer genetic testing, (Table S2, Walsh et al. 2011. PubMed ID: 22006311; Table 1, Loveday et al. 2012. PubMed ID: 22538716; Table 2, Scheckenbach et al. 2013. PubMed ID: 24315737; Table S1, Susswein et al. 2015. PubMed ID: 26681312; Table 2, Yurgelun et al. 2018. PubMed ID: 29961768; Table 1, Li et al. 2019. PubMed ID: 30949688;). RT-PCR analysis and minigene assays suggest this variant results in the in-frame skipping of exon 5 (Table 1, Davy et al. 2017. PubMed ID: 28905878; Sanoguera-Miralles et al. 2020. PubMed ID: 33333735). This variant is reported in 0.0046% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-56787218-A-G). It is interpreted as pathogenic and likely pathogenic in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/128209/). Variants that disrupt the consensus splice acceptor site in RAD51C are expected to be pathogenic. This variant is interpreted as pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

May 08, 2022

Variant summary: RAD51C c.706-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes the canonical 3' splice acceptor site. Experimental evidence demonstrated that this variant affects mRNA splicing leading to the loss of 44 amino acids in a functional domain of the protein by an in-frame exon 5 skipping (Golmard_2013). The variant allele was found at a frequency of 2e-05 in 251368 control chromosomes. c.706-2A>G has been reported in the literature in multiple individuals affected with Breast and Ovarian Cancer (example, Couch_2015, Golmard_2013). These data indicate that the variant is very likely to be associated with disease. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with complete concordance as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.27
Cadd	Pathogenic	34
Dann	Uncertain	0.98
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.97
FATHMM_MKL	Uncertain	0.94	D
MutationTaster	Benign	1.0	D;D
GERP RS		6.0

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.54		Position offset: 12
DS_AL_spliceai		1.0		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs587780259; hg19: chr17-56787218;