chr8-89971232-G-A

Position:

chr8-89971232-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_002485.5(NBN):c.643C>T(p.Arg215Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00306 in 1,613,094 control chromosomes in the GnomAD database, including 11 homozygotes. 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 0.0020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 11 hom. )

Consequence

NBN
NM_002485.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:8B:13O:3

Conservation

PhyloP100: 1.63

Variant links:

Genes affected

NBN (HGNC:7652): (nibrin) Mutations in this gene are associated with Nijmegen breakage syndrome, an autosomal recessive chromosomal instability syndrome characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. The encoded protein is a member of the MRE11/RAD50 double-strand break repair complex which consists of 5 proteins. This gene product is thought to be involved in DNA double-strand break repair and DNA damage-induced checkpoint activation. [provided by RefSeq, Jul 2008]

NBN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.05029258).

BP6

Variant 8-89971232-G-A is Benign according to our data. Variant chr8-89971232-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 6948.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=6, Benign=4, not_provided=3, Uncertain_significance=4}. Variant chr8-89971232-G-A is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00204 (310/152148) while in subpopulation NFE AF= 0.00359 (244/67988). AF 95% confidence interval is 0.00322. There are 0 homozygotes in gnomad4. There are 154 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 11 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBN	NM_002485.5 linkuse as main transcript	c.643C>T	p.Arg215Trp	missense_variant	6/16	ENST00000265433.8	NP_002476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBN	ENST00000265433.8 linkuse as main transcript	c.643C>T	p.Arg215Trp	missense_variant	6/16	1	NM_002485.5	ENSP00000265433	P1

Frequencies

GnomAD3 genomes

AF:

0.00204

AC:

310

AN:

152030

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000459

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00199

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00359

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00251

AC:

630

AN:

250856

Hom.:

AF XY:

0.00251

AC XY:

341

AN XY:

135642

show subpopulations

Gnomad AFR exome

AF:

0.000309

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000653

Gnomad FIN exome

AF:

0.00333

Gnomad NFE exome

AF:

0.00422

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00317

AC:

4624

AN:

1460946

Hom.:

Cov.:

AF XY:

0.00302

AC XY:

2195

AN XY:

726782

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.00168

Gnomad4 ASJ exome

AF:

0.000192

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.00274

Gnomad4 NFE exome

AF:

0.00380

Gnomad4 OTH exome

AF:

0.00234

GnomAD4 genome

AF:

0.00204

AC:

310

AN:

152148

Hom.:

Cov.:

AF XY:

0.00207

AC XY:

154

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.000458

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00199

Gnomad4 NFE

AF:

0.00359

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00273

Hom.:

Bravo

AF:

0.00198

TwinsUK

AF:

0.00458

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00372

AC:

ExAC

AF:

0.00293

AC:

355

EpiCase

AF:

0.00349

EpiControl

AF:

0.00439

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:8Benign:13Other:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Microcephaly, normal intelligence and immunodeficiency

Pathogenic:1Uncertain:2Benign:4Other:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 2006	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Likely benign, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	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 â€šÃ„ÃºWith other alleleâ€šÃ„Ã¹, 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. -
not provided, no classification provided	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	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. -
Likely benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jun 10, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 10, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Mar 24, 2017	- -

not provided

Uncertain:4Benign:3

Benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 21, 2022	- -
Benign, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 07, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 26, 2023	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. -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	NBN: BP4, BS2 -

Hereditary cancer-predisposing syndrome

Uncertain:2Benign:3

Uncertain significance, criteria provided, single submitter	clinical testing	GeneKor MSA	Aug 01, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 28, 2019	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. -
Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	May 03, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	Sep 27, 2021	- -
Likely benign, no assertion criteria provided	clinical testing	True Health Diagnostics	Sep 05, 2017	- -

not specified

Benign:2Other:1

not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 01, 2019	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 be -
Likely benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 12, 2021	- -

NBN-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 11, 2024

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Uncertain

0.040

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.53

D;T;.;.

Eigen

Uncertain

0.49

Eigen_PC

Uncertain

0.42

FATHMM_MKL

Benign

0.097

LIST_S2

Uncertain

0.95

D;D;D;D

M_CAP

Benign

0.048

MetaRNN

Benign

0.050

T;T;T;T

MetaSVM

Uncertain

0.054

MutationAssessor

Uncertain

2.4

M;.;.;.

MutationTaster

Benign

9.0e-8

A;A

PrimateAI

Benign

0.34

PROVEAN

Uncertain

-4.1

D;D;D;D

REVEL

Uncertain

0.34

Sift

Uncertain

0.015

D;D;D;D

Sift4G

Benign

0.14

T;T;T;.

Polyphen

1.0

D;.;.;.

Vest4

0.63

MVP

0.92

MPC

0.41

ClinPred

0.049

GERP RS

5.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.13

gMVP

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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