Submissions for variant NM_002485.5(NBN):c.643C>T (p.Arg215Trp)

gnomAD frequency: 0.00206  dbSNP: rs34767364

Total submissions: 25

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000007363	SCV000166524	benign	Microcephaly, normal intelligence and immunodeficiency	2024-01-31	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000115802	SCV000184001	likely benign	Hereditary cancer-predisposing syndrome	2019-04-28	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Eurofins Ntd Llc (ga)	RCV000487932	SCV000231654	uncertain significance	not provided	2018-06-07	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000487932	SCV000575564	likely benign	not provided	2024-08-01	criteria provided, single submitter	clinical testing	NBN: BP4, BS2
Genetic Services Laboratory, University of Chicago	RCV000121621	SCV000595910	likely benign	not specified	2021-10-12	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000487932	SCV000601698	benign	not provided	2022-02-21	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000487932	SCV000604434	uncertain significance	not provided	2023-10-26	criteria provided, single submitter	clinical testing	The NBN c.643C>T; p.Arg215Trp variant (rs34767364) is reported in the literature in individuals affected with melanoma, breast/ovarian cancer, and Nijmegen breakage syndrome (Berardinelli 2013, Bhai 2021, de Oliveira 2022, Gao 2013, Seemanova 2006). Meta-analysis suggested a cancer-risk of this variant with an odds ratio of 1.7 (Gao 2013). In vitro functional analyses demonstrate a modifying deleterious effect when co-occurring with a pathogenic variant in trans (Seemanova 2006). A breast cancer cell line carrying this variant in hemizygous state has impaired function of NBN (Schroder-Heurich 2014). Additionally, heterozygous p.Arg215Trp B cells were reported to have comparable NBN function and radiosensitivity compared to control cells (Dzikiewicz-Krawczyk 2012). This variant is also reported in ClinVar (Variation ID: 6948) and is found in the non-Finnish European population with an allele frequency of 0.4% (521/128796 alleles, including 3 homozygotes) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.343). Due to conflicting information, the clinical significance of the NBN c.643C>T; p.Arg215Trp variant is uncertain at this time. References: Berardinelli et al. NBN Gene Polymorphisms and Cancer Susceptibility: A Systemic Review. Curr Genomics. 2013 Nov;14(7):425-40. PMID: 24396275. Bhai P et al. Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach. Front Genet. 2021 Jul 13;12:698595. PMID: 34326862. de Oliveira JM et al. The genetics of hereditary cancer risk syndromes in Brazil: a comprehensive analysis of 1682 patients. Eur J Hum Genet. 2022 Jul;30(7):818-823. PMID: 35534704. di Masi A, et al. The R215W mutation in NBS1 impairs gamma-H2AX binding and affects DNA repair: molecular bases for the severe phenotype of 657del5/R215W Nijmegen breakage syndrome patients. Biochem Biophys Res Commun. 2008 May 9;369(3):835-40. PMID: 18328813. Dzikiewicz-Krawczyk A et al. Impact of heterozygous c.657-661del, p.I171V and p.R215W mutations in NBN on nibrin functions. Mutagenesis. 2012 May;27(3):337-43. PMID: 22131123. Gao P et al. Functional variants in NBS1 and cancer risk: evidence from a meta-analysis of 60 publications with 111 individual studies. Mutagenesis. 2013 Nov;28(6):683-97. PMID: 24113799. Schroder-Heurich B et al. Functional deficiency of NBN, the Nijmegen breakage syndrome protein, in a p.R215W mutant breast cancer cell line. BMC Cancer. 2014 Jun 13;14:434. PMID: 24928521. Seemanova E et al. Nijmegen breakage syndrome (NBS) with neurological abnormalities and without chromosomal instability. J Med Genet. 2006 Mar;43(3):218-24. PMID: 16033915.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000121621	SCV000697976	benign	not specified	2019-11-01	criteria provided, single submitter	clinical testing	Variant summary: NBN c.643C>T (p.Arg215Trp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0025 in 269024 control chromosomes, predominantly at a frequency of 0.0042 within the Non-Finnish European subpopulation in the gnomAD database, including 3 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 34 fold of the estimated maximal expected allele frequency for a pathogenic variant in NBN causing Hereditary Breast and Ovarian Cancer phenotype (0.00013), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. However, the frequency in general population is in sub-polymorphic range and these data alone cannot rule out the possibility that it can still have a role as a risk variant in disease, although it has not been reported to have a considerably significant association with other forms of cancer (Taylor_2003, Hebbring_2006, Bogdanovaas_2008, Dzikiewicz-Krawczyk_2012, and Ramus_2014). This is consistent with studies reporting 95% CI around the OR to include 1.0, thereby providing little to no confidence on the strength of the assertions. Specifically, this variant was not significantly associated with increased risk for breast cancer (Bogdanova_2008) (adjusted OR = 1.9, 95%CI 0.84.6, p = 0.18) or prostate cancer (Hebbring_Cancer Epidemiol Biomarkers_2006) (OR = 1.24, 95CI 0.31-4.99, p = 0.77). Functional studies in compound heterozygotes with the 675del5 mutation have shown this variant to affect DNA repair and protein stability, however it is difficult from those studies to make conclusions about the effect of NBN Arg215Trp alone (Seemanova_2006, Bogdanova_2008, di Masi_2008, Mendez_2012). In addition, the variant did not increase chromosome breakage in cells (Seemanova_2006). It was found in a triple negative breast cancer cell line with alternate molecular basis for disease attributed to BRCA1, p.R715X mutation. Although the tumor specimen showed LOH for this NBN variant, the tumor histological characteristics and sensitivity of the cell line to PARP inhibitors can be attributed to the BRCA1 variant. Therefore, the overall implication of these functional data in causation of the NBS or cancer phenotype needs to be further clarified or is unknown (Schroder-Heurich_2014). Meanwhile, functional assays from heterozygous carriers of this variant have also shown the evidences of functional impairment (such as reduced expression of full-length nibrin, impairment in binding with gamma-H2AX and reduction in DNA-DSB rejoining) [Seemanova_2006, di Masi_2006, Dzikiewicz-Krawczyk_2012, and Schroder-Heurich_2014]. From a cell line that also carried BRCA1 p.R1751X, Schroder-Heurich_2014, reports that the (i) cells were highly radiosensitive, susceptible to apoptosis and were deficient in the formation of NBN foci, (ii) NBN was observed only at 30-40% of wildtype levels in the cells; and (iii) there was also evidence for some impairment in the formation of H2AX, MDC1, and 53BP1 foci after irradiation; and these foci appeared smaller and irregular compared with repair foci in wild-type cells, although ATM signaling was largely unaffected. The authors report that these functional consequences related to NBN are not explained by the BRCA1 mutation. This variant has been found in two severely NBS-affected siblings who were compound heterozygous for this variant and 657del5 (Seemanova_2006), although without increased chromosome breakage. Co-occurrences with other pathogenic variants have been reported (TP53 c.783-1G>A; BRCA2 c.8537_8538del, p.Glu2846Glyfs*22) (Yurgelun_2017, Tung_2016), providing supporting evidence for a benign role. 13 ClinVar submitters (evaluation after 2014) classified the variant as benign (1x), likely benign (4x), VUS (7x) and Pathogenic (1x). Based on the evidence outlined above, the variant was classified as benign.
Counsyl	RCV000007363	SCV000800508	uncertain significance	Microcephaly, normal intelligence and immunodeficiency	2017-03-24	criteria provided, single submitter	clinical testing
GeneKor MSA	RCV000115802	SCV000822089	uncertain significance	Hereditary cancer-predisposing syndrome	2018-08-01	criteria provided, single submitter	clinical testing
Mendelics	RCV000007363	SCV000838311	likely benign	Microcephaly, normal intelligence and immunodeficiency	2018-07-02	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000007363	SCV001737335	likely benign	Microcephaly, normal intelligence and immunodeficiency	2021-06-10	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000487932	SCV002011226	benign	not provided	2021-11-03	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000115802	SCV002536700	likely benign	Hereditary cancer-predisposing syndrome	2021-05-03	criteria provided, single submitter	curation
OMIM	RCV000007363	SCV000027562	pathogenic	Microcephaly, normal intelligence and immunodeficiency	2006-03-01	no assertion criteria provided	literature only
ITMI	RCV000121621	SCV000085819	not provided	not specified	2013-09-19	no assertion provided	reference population
GeneReviews	RCV000007363	SCV000494626	not provided	Microcephaly, normal intelligence and immunodeficiency		no assertion provided	literature only
True Health Diagnostics	RCV000115802	SCV000788081	likely benign	Hereditary cancer-predisposing syndrome	2017-09-05	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003891431	SCV000806447	likely benign	NBN-related disorder	2024-03-11	no assertion criteria provided	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc.	RCV000007363	SCV001457051	uncertain significance	Microcephaly, normal intelligence and immunodeficiency	2020-01-10	no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000007363	SCV001549892	likely benign	Microcephaly, normal intelligence and immunodeficiency		no assertion criteria provided	clinical testing	The NBN p.Arg215Trp variant was identified in 53 of 18583 proband chromosomes (frequency: 0.003) from Australian, North American, French Canadian, Macedonian, German, Belarusian, and Polish individuals or families with breast, ovarian or other cancers and was present in 19 of 15624 control chromosomes (frequency: 0.001) from healthy individuals (Damiola 2014, Desjardins 2009, Kostovska 2015, Bogdanova 2007, Steffen 2004, Ramus 2015, Kurian 2014). The variant was also identified in dbSNP (ID: rs34767364) as “With other allele”, ClinVar (classified with conflicting interpretations of pathogenicity including benign by Invitae, Color Genomics; likely benign by Ambry Genetics, ARUP Laboratories; uncertain significance by EGL Genetic Diagnostics, Genetic Services Laboratory-University of Chicago, Quest Diagnostics Nichols Institute San Juan Capistrano, Laboratory Corporation of America and Praxis fuer Humangenetik Tuebingen; pathogenic by GeneReviews and OMIM; and classification not provided by ITMI), Clinvitae (5x), LOVD 3.0 (1x), Zhejiang University Database (24x , co-occurring with pathogenic NBN variant c.657_661del/p.Lys219AsnfsX16), and was not identified in Cosmic. The variant was identified in control databases in 671 of 276666 chromosomes (3 homozygous) at a frequency of 0.002 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 14 of 24000 chromosomes (freq: 0.0006), Other in 16 of 6452 chromosomes (freq: 0.002), Latino in 55 of 34344 chromosomes (freq: 0.002), European Non-Finnish in 502 (3 homozygous) of 126366 chromosomes (freq: 0.004), Ashkenazi Jewish in 3 of 10136 chromosomes (freq: 0.0003), Finnish in 79 of 25738 chromosomes (freq: 0.003), and South Asian in 2 of 30780 chromosomes (freq: 0.00007); it was not in the East Asian population. There is conflicting evidence in the literature as studies utilizing breast cancer cell lines from a heterozygous breast cancer patient carrying the variant and a truncating BRCA1 variant showed a 70% reduction of NBN protein expression, which was not seen in a BRCA1 cell line with wildtype NBN (Bogdanova 2007, Schroder-Heurich 2014). Seemanova et al (2005) also describe a dosage effect in twin boys affected with Nijmegen breakage syndrome, who are compound heterozygotes (with the founder mutation NBN 657del5), whereby the variant produced full length nibrin, but addition of the nonpolar Trp may still be associated with protein instability. In a large meta-analysis encompassing 60 independent publications, the variant was related to susceptibility to all cancers, but no significant risk was observed for breast cancer (Gao 2013). The p.Arg215 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact of the variant Trp to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
GenomeConnect - Invitae Patient Insights Network	RCV000007363	SCV001749669	not provided	Microcephaly, normal intelligence and immunodeficiency		no assertion provided	phenotyping only	Variant interpreted as Uncertain significance and reported on 05-24-2017 by Myriad. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000487932	SCV001807367	uncertain significance	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000487932	SCV001960031	uncertain significance	not provided		no assertion criteria provided	clinical testing
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	RCV000115802	SCV001977051	uncertain significance	Hereditary cancer-predisposing syndrome	2021-09-27	no assertion criteria provided	clinical testing