ClinVar Miner

Submissions for variant NM_002485.4(NBN):c.1690G>A (p.Glu564Lys) (rs72550742)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212749 SCV000170641 benign not specified 2014-02-07 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000129092 SCV000183802 likely benign Hereditary cancer-predisposing syndrome 2018-09-27 criteria provided, single submitter clinical testing Subpopulation frequency in support of benign classification;Co-occurence with mutation in same gene (phase unknown)
Invitae RCV000205604 SCV000261407 benign Microcephaly, normal intelligence and immunodeficiency 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000129092 SCV000685731 likely benign Hereditary cancer-predisposing syndrome 2015-06-02 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589500 SCV000697949 benign not provided 2016-03-21 criteria provided, single submitter clinical testing Variant summary: The NBN c.1690G>A variant affects a conserved nucleotide, resulting in amino acid change from Glu to Lys. 3/4 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index). Functional studies have not been carried out to prove or disprove these in silico predictions. The variant of interest was observed in a large, broad control population, ExAC, with an allele frequency of 118/121386 (1/1028), predominantly found in the East Asian cohort, 91/8654 (1/95), which exceeds the predicted maximum expected allele frequency for a pathogenic NBN variant of 1/8000 for HBOC. Therefore, suggesting that the variant of interest is a common polymorphism found in population(s) of East Asian origin. The variant has also been cited in cancer patients of East Asian origin, but without evidence of causality (i.e. co-segregation data). In addition, several clinical laboratories classified this variant as benign/likely benign. Taken together, the variant of interest was classified as Benign.
Counsyl RCV000205604 SCV000788524 likely benign Microcephaly, normal intelligence and immunodeficiency 2017-01-10 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589500 SCV000888326 benign not provided 2019-01-25 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000589500 SCV001245907 likely benign not provided 2019-07-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000205604 SCV001324788 benign Microcephaly, normal intelligence and immunodeficiency 2017-08-21 criteria provided, single submitter clinical testing 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

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