rs61754966

chr8-89978293-T-Cchr8-89978293-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_002485.5(NBN):c.511A>G(p.Ile171Val) variant causes a missense change. The variant allele was found at a frequency of 0.00115 in 1,593,902 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I171L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0014 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0011 (5 hom.)
• Consequence: NBN NM_002485.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:15 B:9 O:2
• Conservation: PhyloP100: 4.37

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.037225217).
• BP6: Variant 8-89978293-T-C is Benign according to our data. Variant chr8-89978293-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 6946.We mark this variant Likely_benign, oryginal submissions are: {not_provided=1, Likely_benign=7, Uncertain_significance=13, Benign=2}. Variant chr8-89978293-T-C is described in Lovd as [Benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00139 (212/152314) while in subpopulation NFE AF= 0.00254 (173/68022). AF 95% confidence interval is 0.00223. There are 1 homozygotes in gnomad4. There are 107 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 5 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBN	NM_002485.5	c.511A>G	p.Ile171Val	missense_variant	5/16	ENST00000265433.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NBN	ENST00000265433.8	c.511A>G	p.Ile171Val	missense_variant	5/16	1	NM_002485.5	P1

Frequencies

GnomAD3 genomes AF: 0.00139 AC: 212 AN: 152196 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00254

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.00120 AC: 301 AN: 251288 Hom.: 0 AF XY: 0.00117 AC XY: 159 AN XY: 135832

Gnomad AFR exome AF: 0.000370

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.000397

Gnomad EAS exome AF: 0.00152

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00120

Gnomad NFE exome AF: 0.00196

Gnomad OTH exome AF: 0.000979

GnomAD4 exome AF: 0.00112 AC: 1618 AN: 1441588 Hom.: 5 Cov.: 28 AF XY: 0.00114 AC XY: 821 AN XY: 718462

Gnomad4 AFR exome AF: 0.0000909

Gnomad4 AMR exome AF: 0.000336

Gnomad4 ASJ exome AF: 0.000231

Gnomad4 EAS exome AF: 0.00327

Gnomad4 SAS exome AF: 0.0000350

Gnomad4 FIN exome AF: 0.00157

Gnomad4 NFE exome AF: 0.00121

Gnomad4 OTH exome AF: 0.000871

GnomAD4 genome AF: 0.00139 AC: 212 AN: 152314 Hom.: 1 Cov.: 33 AF XY: 0.00144 AC XY: 107 AN XY: 74472

Gnomad4 AFR AF: 0.000265

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00254

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00194 Hom.: 1

Bravo AF: 0.000907

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.00163 AC: 14

ExAC AF: 0.00139 AC: 169

Asia WGS AF: 0.00144 AC: 5 AN: 3476

EpiCase AF: 0.000927

EpiControl AF: 0.00119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:15 Benign:9 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4 Benign:3

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 03, 2021	This variant is associated with the following publications: (PMID: 21811815, 11325820, 30306255, 17695489, 28374160, 30651582, 31422574, 21698754, 19813148, 25862857, 23317186, 22373003, 16474176, 21436738, 19629396, 21472885, 19393249, 24396275, 25712764, 25619955, 15279809, 18056440, 15338273, 16810201, 26083025, 25980754, 19908051, 17899368, 19523210, 24093751, 18280732, 24113799, 24728327, 24830725, 22131123, 26722329, 27621404, 18049891, 28261280, 27616075, 28376765, 27153395, 28591191, 28076423, 28107384, 29335925, 31159747, 32019277, 30590007, 31278556, 31263571, 32566746) -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 27, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 16, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2024	NBN: BP4, BS1:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 09, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 07, 2017	The NBN c.511A>G;p.Ile171Val variant has been published in the medical literature in individuals with various cancers and has been shown to be associated with increased cancer development risk (Desjardins 2009, Gao 2013, Grajkowska 2009, Kaluzna 2015, Mosor 2013, Nowak 2008, Shimada 2004, Varon 2001). However, this variant has also been described as occurring at a similar frequency in affected and unaffected individuals and shown to have no significant association with cancer risk (Zhang 2012). The variant is listed in the ClinVar database (Variation ID: 6946) and the dbSNP variant database (rs61754966) with an allele frequency of 0.123 percent (16/12990 alleles) in the Exome Variant Server and 0.1509 percent (418/277070 alleles) in the Genome Aggregation Database. The amino acid at this position is highly conserved among species, is predicted to reside in a critical functional domain, and computational algorithms (PolyPhen2, SIFT) predict this variant is deleterious. Some functional studies do show a significant functional impairment, while others show no significant change (Dzikiewicz 2012, Yamamoto 2014). Due to conflicting information, it is unclear if this variant is benign or a low penetrance pathogenic allele. Therefore, the clinical significance of this variant cannot be determined with certainty. If this variant is later determined to be pathogenic, this individual may be at increased risk for development of breast cancer (OMIM#602667). References: Desjardins S et al. Variations in the NBN/NBS1 gene and the risk of breast cancer in non-BRCA1/2 French Canadian families with high risk of breast cancer. BMC Cancer. 2009 Jun 12;9:181. 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. 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. Grajkowska W et al. Ganglioglioma associated with alterations of NBN gene. A case report. Folia Neuropathol. 2009;47(3):278-83. Kaluzna EM et al. Heterozygous p.I171V mutation of the NBN gene as a risk factor for lung cancer development. Oncol Lett. 2015 Nov;10(5):3300-3304. Kraus C et al. Gene panel sequencing in familial breast/ovarian cancer patients identifies multiple novel mutations also in genes others than BRCA1/2. Int J Cancer. 2017 Jan 1;140(1):95-102. Mosor M et al. Germline variants in MRE11/RAD50/NBN complex genes in childhood leukemia. BMC Cancer. 2013 Oct 5;13:457. Nowak J et al. Heterozygous carriers of the I171V mutation of the NBS1 gene have a significantly increased risk of solid malignant tumours. Eur J Cancer. 2008 Mar;44(4):627-30. Shimada H et al. First case of aplastic anemia in a Japanese child with a homozygous missense mutation in the NBS1 gene (I171V) associated with genomic instability. Hum Genet. 2004 Oct;115(5):372-6. Varon R et al. Mutations in the Nijmegen Breakage Syndrome gene (NBS1) in childhood acute lymphoblastic leukemia (ALL). Cancer Res. 2001 May 1;61(9):3570-2. Yamamoto Y et al. A rare polymorphic variant of NBS1 reduces DNA repair activity and elevates chromosomal instability. Cancer Res. 2014 Jul 15;74(14):3707-15. Zhang ZH et al. Current evidence on the relationship between two polymorphisms in the NBS1 gene and breast cancer risk: a meta-analysis. Asian Pac J Cancer Prev. 2012;13(11):5375-9. -

Hereditary cancer-predisposing syndrome Uncertain:3 Benign:2

Likely benign, criteria provided, single submitter	curation	Sema4, Sema4	Apr 20, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneKor MSA	Aug 01, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneID Lab - Advanced Molecular Diagnostics	Sep 07, 2017	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 24, 2022	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. -
Uncertain significance, criteria provided, single submitter	research	Department of Pediatric Oncology, Hematology and Clinical Immunology, University Clinics Duesseldorf	-	- -

Microcephaly, normal intelligence and immunodeficiency Uncertain:3 Benign:1

Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Apr 03, 2020	- -

not specified Uncertain:1 Benign:1 Other: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	Apr 10, 2019	Variant summary: NBN c.511A>G (p.Ile171Val) results in a conservative amino acid change located in the BRCT domain of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0016 in 287466 control chromosomes, predominantly at a frequency of 0.0026 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 21 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. c.511A>G has been reported in the literature in individuals affected with Breast and Ovarian Cancer, various forms of leukemia and solid tumors (example Taylor_2003, Bogdanova_2008, Grajkowska_2009, Haiman_2013, Kaluzna_2015, Kim_2015, Ramus_2015). Several of these predate the emergence of large control datasets such as ExAC and gnomAD. Predominantly, these report(s) do not provide unequivocal conclusions about the association of the variant with Hereditary Breast and Ovarian Cancer. Furthermore, reports of association with other forms of leukemia and solid tumors have not been firmly established. Co-occurrences with other pathogenic variant(s) in multiple genes have been reported in the literature as well as in our own testing experience. Specifically, BRCA1 c.3700_3704delGTAAA, p.Val1234Glnfs (Domagala_2015); CHEK2 c.444+1G>A (Domagala_2015; BRCA2 c.6952C>T, p.Arg2318X (Internal testing); BRCA1, not specified; and PALB2, not specified (Koczkowska_2018). These co-occurrences provide additional supporting evidence for a benign role. Multiple publications provide conflicting experimental evidence evaluating an impact on protein function. Most report no difference in measures of radiation induced DNA damage (Dzikiewicz-Krawczyk_2012), cell cycle mediated DNA synthesis and chromosomal instability (Dzikiewicz-Krawczyk_2012, Nowak_2017). The most pronounced variant effect results in reduced double stranded repair (DSB) activity through loss of association with MDC1 (Yamamoto_2014). Thirteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments ranging from benign/likely benign (n=2) to uncertain significance (n=11) using the same literature assessed in the scope of this evaluation. Based on the evidence outlined above, the variant was classified as benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Dec 12, 2014	- -

Aplastic anemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Oct 01, 2004

- -

Carcinoma of colon Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The NBN p.Ile171Val variant was identified in 84 of 9038 proband chromosomes (frequency: 0.01) from individuals or families with acute lymphoblastic leukemia, lung cancer, breast and ovarian cancer, head and neck cancer, colorectal cancer, aplastic anemia and other hematological malignancies and was not identified in 220 control chromosomes from healthy individuals (Varon 2001, Kaluzna 2015, Desjardins 2009, Ziolkowska 2007, Nowak 2008, Bogdanova 2008, Kanka 2007). The variant was also identified in the following databases: ClinVar (1x pathogenic: OMIM 1x “risk factor”; 4x uncertain significance: GeneDx, Ambry Genetics, Emory Genetics, University of Chicago; 1x benign Invitae; 1x not provided ITMI), LOVD 3.0 (1x not classified), and the Zhejiang University database (5x probably pathogenic, 1x pathogenic). The variant was not identified in the COSMIC database. The variant was identified in control databases in 418 of 277070 chromosomes at a frequency of 0.002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017); it was identified in the following populations: European (Non-Finnish) in 327 of 126600 chromosomes (frequency 0.003), European (Finnish) in 37 of 25785 chromosomes (frequency 0.001), East Asian in 27 of 18870 chromosomes (frequency 0.001), Other in 8 of 6458 chromosomes (frequency 0.001), Ashkenazi Jewish in 4 of 10148 chromosomes (frequency 0.0004), African in 6 of 24026 chromosomes (frequency 0.0002), Latino in 8 of 34404 chromosomes (frequency 0.0002), and South Asian in 1 of 30782 chromosomes (frequency 0.00003). A Japanese child with aplastic anemia has been found to be homozygous for this variant. Lymphoblastoid cell lines from this patient and her carrier father showed increased polyploidy. In addition, the homozygous patient had higher frequency of chromosomal structural aberrations than her heterozygous father and had an intermediate frequency of chromosomal structural aberrations compared to that of the patient and controls, suggesting that the variant may affect genomic integrity in hematopoietic cells (Shimada 2004). However the patient had no features of Nijmegen breakage syndrome. The p.Ile171Val residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. 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. -

Acute lymphoid leukemia Uncertain:1

Uncertain significance, criteria provided, single submitter

reference population

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

Mar 18, 2016

- -

Hereditary breast ovarian cancer syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Cancer Genomics Group, Japanese Foundation For Cancer Research

May 01, 2019

- -

Breast carcinoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jan 01, 2019

- -

NBN-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 27, 2023

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). -

Hereditary cancer Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

Jan 23, 2024

- -

Leukemia, acute lymphoblastic, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Oct 01, 2004

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Uncertain	-0.060
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.15	T;T;.;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.80	T;T;T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.037	T;T;T;T
MetaSVM	Benign	-0.55	T
MutationAssessor	Pathogenic	3.0	M;.;.;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.80	N;N;N;N
REVEL	Uncertain	0.40
Sift	Pathogenic	0.0	D;D;T;T
Sift4G	Pathogenic	0.0	D;D;.;D
Polyphen		1.0	D;.;.;.
Vest4		0.40
MVP		0.68
MPC		0.087
ClinPred		0.11	T
GERP RS		4.8
Varity_R		0.39
gMVP		0.53

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

Other links and lift over

dbSNP: rs61754966; hg19: chr8-90990521; COSMIC: COSV104545444; COSMIC: COSV104545444;