ClinVar Miner

Submissions for variant NM_002485.5(NBN):c.-10A>T

gnomAD frequency: 0.00004  dbSNP: rs759094270
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586130 SCV000697936 uncertain significance not provided 2017-03-03 criteria provided, single submitter clinical testing Variant summary: The NBN c.-10A>T variant involves the alteration of a non-conserved nucleotide in the 5 region. One in silico tool predicts a benign outcome for this variant. 3/5 splice prediction tools predict a gain of cryptic splicing donor site. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 1/109698 control chromosomes at a frequency of 0.0000091, which does not exceed the estimated maximal expected allele frequency of a pathogenic NBN variant (0.0025). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586130 SCV000889541 uncertain significance not provided 2018-04-18 criteria provided, single submitter clinical testing
GeneDx RCV000586130 SCV001856885 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001800804 SCV002046015 likely benign Microcephaly, normal intelligence and immunodeficiency 2021-11-07 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003420019 SCV004117643 uncertain significance NBN-related disorder 2022-10-20 criteria provided, single submitter clinical testing The NBN c.-10A>T variant is located in the 5' untranslated region. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0048% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/8-90996799-T-A). In ClinVar, this variant is interpreted as benign/likely benign/uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/492068/?new_evidence=false). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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