ClinVar Genomic variation as it relates to human health

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

This variant is associated with the following publications: (PMID: 23525077, 26976419, 27443514, 23555315)

Variant summary: NBN c.1036G>A (p.Val346Met) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0003 in 251374 control chromosomes, predominantly at a frequency of 0.0033 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in NBN causing Nijmegen Breakage Syndrome phenotype (0.0025), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.1036G>A has been reported in the literature in individuals affected with breast cancer, endometrial cancer and in unaffected controls (example, Haiman_2013, Tung_2016, Ring_2016, Momozawa_2018). These reports do not provide unequivocal conclusions about association of the variant with Nijmegen Breakage Syndrome or with any of the NBN associated tumors. At-least two co-occurrences with other pathogenic variants have been observed at our laboratory (APC c.1206_1207delTG, p.Glu403AsnfsX15; BRCA2 c.6405_6409delCTTAA, p.Asn2135LysfsX3), providing additional supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 23555315, 26976419, 27443514, 30287823). Fourteen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as likely benign (n=9) and VUS (n=5). Based on the evidence outlined above, the variant was classified as likely benign.

The allele frequency of this variant c.1036G>A (p.Val346Met) is 0.003 in East Asian of gnomAD Exomes and 0.002 in East Asian in 1000 Genomes. There is a small physicochemical difference between valine and methionine, which is not likely to impact secondary protein structure as these residues share similar properties. The variant is predicted to be tolerated by both SIFT or PolyPhen2. For these reasons, this variant has been classified as Likely Benign.

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.

The NBN p.Val346Met variant was identified in 1 of 976 proband chromosomes (frequency: 0.001) from individuals or families with breast cancer (Tung 2016). The variant was also identified in the following databases: dbSNP (ID: rs200297914) as “With Uncertain significance allele”, in ClinVar (classified with conflicting interpretations of pathogenicity; submitters: likely benign by Invitae and uncertain significance by GeneDx, Ambry Genetics, EGL Genetic Diagnostics and Laboratory Corporation of America), Clinvitae (4x), Cosmic (1x in an adenocarcinoma of the oesophagus), and not identified in LOVD 3.0 and Zhejiang University Database. The variant was identified in control databases in 77 of 277100 chromosomes at a frequency of 0.0003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: Latino in 3 of 34386 chromosomes (freq: 0.00009), European Non-Finnish in 2 of 126628 chromosomes (freq: 0.00002), East Asian in 62 of 18866 chromosomes (freq: 0.003), and South Asian in 10 of 30782 chromosomes (freq: 0.0003); it was not observed in the African, Other, Ashkenazi Jewish and Finnish populations. The p.Val346 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact of the variant Met to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 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. 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.

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).