ClinVar Miner

Submissions for variant NM_002485.5(NBN):c.171+4T>C

gnomAD frequency: 0.00001  dbSNP: rs587782290
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000131170 SCV000186116 likely benign Hereditary cancer-predisposing syndrome 2021-05-21 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
Invitae RCV000205676 SCV000259796 likely benign Microcephaly, normal intelligence and immunodeficiency 2023-12-13 criteria provided, single submitter clinical testing
GeneDx RCV000590607 SCV000518617 likely benign not provided 2019-03-08 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 29368341)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590607 SCV000697950 uncertain significance not provided 2016-12-22 criteria provided, single submitter clinical testing Variant summary: The NBN c.171+4T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 3/5 splice prediction tools predict strengthen effect on a canonical splicing donor site, and ESEfinder predicts change of binding site for SR055. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/121362 control chromosomes at a frequency of 0.0000247, which does not exceed the estimated maximal expected allele frequency of a pathogenic NBN variant (0.0025). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.
Counsyl RCV000205676 SCV000789324 uncertain significance Microcephaly, normal intelligence and immunodeficiency 2017-01-25 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000590607 SCV000806416 likely benign not provided 2017-03-17 criteria provided, single submitter clinical testing
Mendelics RCV000205676 SCV000838319 uncertain significance Microcephaly, normal intelligence and immunodeficiency 2018-07-02 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000205676 SCV002045985 uncertain significance Microcephaly, normal intelligence and immunodeficiency 2021-11-07 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000131170 SCV002536616 uncertain significance Hereditary cancer-predisposing syndrome 2021-10-08 criteria provided, single submitter curation

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