rs61754796

chr8-89971247-C-Achr8-89971247-C-Gchr8-89971247-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS1

The NM_002485.5(NBN):c.628G>T(p.Val210Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000756 in 1,613,198 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. V210L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00049 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00078 (1 hom.)
• Consequence: NBN NM_002485.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:12 B:8 O:2
• Conservation: PhyloP100: -0.408

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 -9 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.034131557).
• BP6: Variant 8-89971247-C-A is Benign according to our data. Variant chr8-89971247-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 127014.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=11, Likely_benign=6, not_provided=2}. Variant chr8-89971247-C-A is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000784 (1145/1460924) while in subpopulation NFE AF= 0.000942 (1047/1111454). AF 95% confidence interval is 0.000894. There are 1 homozygotes in gnomad4_exome. There are 552 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBN	NM_002485.5	c.628G>T	p.Val210Phe	missense_variant	6/16	ENST00000265433.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NBN	ENST00000265433.8	c.628G>T	p.Val210Phe	missense_variant	6/16	1	NM_002485.5	P1

Frequencies

GnomAD3 genomes AF: 0.000480 AC: 73 AN: 152156 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000926

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000403 AC: 101 AN: 250916 Hom.: 0 AF XY: 0.000398 AC XY: 54 AN XY: 135684

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.0000925

Gnomad NFE exome AF: 0.000767

Gnomad OTH exome AF: 0.000327

GnomAD4 exome AF: 0.000784 AC: 1145 AN: 1460924 Hom.: 1 Cov.: 30 AF XY: 0.000759 AC XY: 552 AN XY: 726798

Gnomad4 AFR exome AF: 0.0000898

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000128

Gnomad4 FIN exome AF: 0.000188

Gnomad4 NFE exome AF: 0.000942

Gnomad4 OTH exome AF: 0.00109

GnomAD4 genome AF: 0.000486 AC: 74 AN: 152274 Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32 AN XY: 74450

Gnomad4 AFR AF: 0.000144

Gnomad4 AMR AF: 0.0000653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.000941

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000666 Hom.: 0

Bravo AF: 0.000552

TwinsUK AF: 0.00216 AC: 8

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00140 AC: 12

ExAC AF: 0.000486 AC: 59

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00115

EpiControl AF: 0.00101

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:12 Benign:8 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:3 Benign:3 Other:1

not provided, no classification provided	literature only	Harris Lab, University of Minnesota	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
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, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 06, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jan 24, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jan 12, 2023	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with a personal or family history of breast, ovarian, and other cancers (Varon et al., 2001; Mosor et al., 2006; Steffen et al., 2006; Meyer et al., 2007; Mateju et al., 2012; Damiola et al., 2014; Ramus et al., 2015; Bueno et al., 2016; Hauke et al., 2018; Zuntini et al., 2021); In a breast cancer case-control analysis, this variant was not observed at a higher frequency in cases vs. controls (Zuntini et al., 2021); Published functional studies suggest a potential impact on DNA repair ability (Zuntini et al., 2021); This variant is associated with the following publications: (PMID: 19452044, 26787654, 16810201, 29522266, 32668560, 24894818, 11325820, 16770759, 24728327, 17496786, 20805886, 22491912, 24396275, 26928227, 26315354, 28873162, 29371908, 12353271, 26564480, 18606567, 29641532, 29844865, 31278556, 19804756, 34426522, 34072463, 30306255, 31780696, 31874108) -

Microcephaly, normal intelligence and immunodeficiency Uncertain:4 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Aug 19, 2021	The NBN c.628G>T (p.Val210Phe) missense change has a maximum subpopulation frequency of 0.076% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/8-90983475-C-A). Five of seven in silico tools predict a benign effect of this variant on protein function (BP4), but to our knowledge these predictions have not been confirmed by functional assays. This variant is present 16x in the FLOSSIES database which contains genetic variants from women older than 70 years of age who have never had cancer (BS2; https://whi.color.com/variant/8-90983475-C-A). In summary, this variant meets criteria to be classified as likely benign based on the ACMG/AMP criteria: BS2, BP4. -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Jan 12, 2022	This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 07, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 29, 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	Mendelics	Jul 02, 2018	- -

not specified Uncertain:2 Benign:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jan 30, 2015	- -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 17, 2023	Variant summary: NBN c.628G>T (p.Val210Phe) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0004 in 267128 control chromosomes, predominantly at a frequency of 0.00077 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 6-fold of the estimated maximal expected allele frequency for a pathogenic variant in NBN causing Hereditary Breast And Ovarian Cancer (HBOC) Syndrome phenotype (0.00013), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.628G>T has been reported in the literature in individuals affected with cancer including HBOC and Acute Lymphoblastic Leukemia (e.g., Varon_2001, Mosor_2006, Steffen_2006, Mateju_2012, Damiola_2015, Ramus_2015, Bonache_2018, Dominguez-Valentin_2018, Hauke_2018, Dutil_2019, Zuntini_2021), but has also been reported in controls (e.g., Mateju_2012, Ramus_2015). These reports therefore do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. A co-occurrence with a pathogenic variant has been observed by our lab (BRCA2 c.9027delT, p.His3010IlefsX18; Internal testing), providing supporting evidence for a benign role. The variant was also reported in 16 women older than age 70 years who have never had cancer (FLOSSIES database) providing further evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (e.g., Zuntini_2021). The following publications have been ascertained in the context of this evaluation (PMID: 24728327, 30306255, 12353271, 26564480, 29371908, 31780696, 29522266, 22491912, 31874108, 16810201, 32668560, 26315354, 16770759, 11325820, 26787654, 34072463). Multiple ClinVar submitters (evaluation after 2014) have reported the variant; eleven submitters cited the variant as uncertain significance and six submitters cited it as likely benign. Based on the evidence outlined above, the variant was classified as likely benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 25, 2019	The NBN c.628G>T; p.Val210Phe variant (rs61754796) is reported in the literature in individuals with melanoma, acute lymphoblastic leukemia, breast or ovarian cancer (Dominguez-Valentin 2018, Mateju 2012, Meyer 2007, Mosor 2006, Ramus 2015, Steffen 2006, Varon 2001), but is also reported in controls (Mateju 2012, Offer 2010, Ramus 2015). This variant is also found in the general population with an overall allele frequency of 0.04% (115/282316 alleles) in the Genome Aggregation Database. This variant is classified as uncertain by multiple laboratories in ClinVar (Variation ID: 127014). The valine at codon 210 is weakly conserved, but computational analyses (SIFT: Damaging, PolyPhen-2: Benign) predict conflicting effects of this variant on protein structure/function. Based on available information, the clinical significance of this variant is uncertain at this time. REFERENCES Dominguez-Valentin M et al. Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds. Hered Cancer Clin Pract. 2018 Jan 15;16:4. Mateju M et al. Germline mutations 657del5 and 643C>T (R215W) in NBN are not likely to be associated with increased risk of breast cancer in Czech women. Breast Cancer Res Treat. 2012 Jun;133(2):809-11. Meyer P et al. Molecular genetic analysis of NBS1 in German melanoma patients. Melanoma Res. 2007 Apr;17(2):109-16. Mosor M et al. Association of the heterozygous germline I171V mutation of the NBS1 gene with childhood acute lymphoblastic leukemia. Leukemia. 2006 Aug;20(8):1454-6. Offer SM et al. Unique DNA repair gene variations and potential associations with the primary antibody deficiency syndromes IgAD and CVID. PLoS One. 2010 Aug 18;5(8):e12260. Ramus SJ et al. Germline Mutations in the BRIP1, BARD1, PALB2, and NBN Genes in Women With Ovarian Cancer. J Natl Cancer Inst. 2015 Aug 27;107(11). Steffen J et al. Germline mutations 657del5 of the NBS1 gene contribute significantly to the incidence of breast cancer in Central Poland. Int J Cancer. 2006 Jul 15;119(2):472-5. 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. -

Hereditary cancer-predisposing syndrome Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 09, 2018	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	Dec 27, 2021	- -

Aplastic anemia;C0023449:Acute lymphoid leukemia;C0398791:Microcephaly, normal intelligence and immunodeficiency Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 23, 2017

- -

NBN-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 22, 2024

The NBN c.628G>T variant is predicted to result in the amino acid substitution p.Val210Phe. This variant has been reported in individuals with a history of acute lymphoblastic leukemia, breast cancer, and ovarian cancer (Mosor et al. 2006. PubMed ID: 16810201; Varon et al. 2001. PubMed ID: 11325820; Mateju et al. 2012. PubMed ID: 22491912; Steffen et al. 2006. PubMed ID: 16770759; Supplementary Table 4, Ramus et al. 2015. PubMed ID: 26315354; Zuntini et al. 2021. PubMed ID: 34072463), but has also been identified in cohorts of unaffected individuals (Supplementary Table 4, Ramus et al. 2015. PubMed ID: 26315354; Table S1, Bodian et al. 2014. PubMed ID: 24728327). This variant is reported in 0.076% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations of likely benign and uncertain significance in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/127014/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The NBN p.Val210Phe variant was identified in 4 of 3654 proband chromosomes (frequency: 0.001) from individuals or families with melanoma, breast cancer, Non-Hodgkin lymphomas, ALL (Meyer_2007, Damiola_2014, Cerosaletti_2002, Varon_2001). The variant was also identified in the following databases: dbSNP (ID: rs61754796) as “With Uncertain significance allele”, ClinVar (classified as uncertain significance by GeneDx, Invitae, GSLUC; classified as likely benign by Ambry Genetics), Clinvitae (classified as uncertain significance by ClinVar, Invitae; classified as likely benign by ClinVar), and the Zhejiang Colon Cancer Database. The variant was not identified in Cosmic or LOVD 3.0, databases. The variant was identified in 116 of 276770 chromosomes at a frequency of 0.0004 in the following populations: African in 3 of 24004 chromosomes (freq. 0.000125), “other” in 3 of 6450 chromosomes (freq. 0.00046), Latino in 4 of 34354 chromosomes (freq. 0.000116), European in 97 of 126420 chromosomes (freq. 0.00076), Finnish in 5 of 25764 chromosomes (freq. 0.0002), and South Asian in 4 of 30782 chromosomes (freq. 0.00013), increasing the likelihood this could be a low frequency benign variant in certain populations (Genome Aggregation Consortium Feb 27, 2017). The p.Val210 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 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. The variant is located with the Nibrin functional domain. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.11
Cadd	Benign	16
Dann	Uncertain	0.98
DEOGEN2	Benign	0.18	T;T;.;.
Eigen	Benign	-0.71
Eigen_PC	Benign	-0.68
FATHMM_MKL	Benign	0.037	N
LIST_S2	Uncertain	0.88	D;D;D;D
M_CAP	Benign	0.077	D
MetaRNN	Benign	0.034	T;T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Benign	1.4	L;.;.;.
MutationTaster	Benign	0.73	N;N
PrimateAI	Benign	0.28	T
PROVEAN	Uncertain	-2.4	N;N;N;D
REVEL	Benign	0.28
Sift	Uncertain	0.0060	D;D;D;D
Sift4G	Uncertain	0.020	D;D;D;.
Polyphen		0.21	B;.;.;.
Vest4		0.58
MVP		0.80
MPC		0.094
ClinPred		0.041	T
GERP RS		-1.9
Varity_R		0.12
gMVP		0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs61754796; hg19: chr8-90983475; COSMIC: COSV99619337;