ClinVar Miner

Submissions for variant NM_002485.4(NBN):c.2082T>G (p.Pro694=) (rs7823648)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000128893 SCV000172753 benign Hereditary cancer-predisposing syndrome 2014-11-20 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Illumina Clinical Services Laboratory,Illumina RCV000350955 SCV000475287 benign Microcephaly, normal intelligence and immunodeficiency 2018-01-12 criteria provided, single submitter clinical testing 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000350955 SCV000562939 benign Microcephaly, normal intelligence and immunodeficiency 2020-11-23 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282150 SCV000604435 benign none provided 2020-07-20 criteria provided, single submitter clinical testing
Color Health, Inc RCV000128893 SCV000685753 benign Hereditary cancer-predisposing syndrome 2015-03-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000507423 SCV000806427 benign not specified 2017-02-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000507423 SCV000888333 benign not specified 2020-07-09 criteria provided, single submitter clinical testing
GeneDx RCV001705925 SCV001916584 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000128893 SCV000788077 likely benign Hereditary cancer-predisposing syndrome 2017-09-11 no assertion criteria provided clinical testing
Natera, Inc. RCV000350955 SCV001456582 benign Microcephaly, normal intelligence and immunodeficiency 2020-09-16 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000507423 SCV001553554 benign not specified no assertion criteria provided clinical testing The NBN p.Pro694= variant was not identified in the literature nor was it identified in the Zhejiang Colon Cancer Database. The variant was identified in the following databases: dbSNP (ID: rs7823648) as other, ClinVar (classified as benign by Ambry genetics, Invitae; classified as likely benign by Illumina), and LOVD 3.0. The variant was identified in control databases in 2107 (77 homozygous) of 277000 chromosomes at a frequency of 0.0076 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: African in 1843 of 24028 chromosomes (freq: 0.077). The p.Pro694= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, 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 this variant meets our laboratory's criteria to be classified as benign.
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000507423 SCV001809357 benign not specified no assertion criteria provided clinical testing

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