ClinVar Miner

Submissions for variant NM_001271208.2(NEB):c.25510-20dup (rs148839798)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000252429 SCV000307333 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000252429 SCV000570649 benign not specified 2016-07-08 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.
Integrated Genetics/Laboratory Corporation of America RCV000590263 SCV000697824 benign not provided 2017-04-24 criteria provided, single submitter clinical testing Variant summary: The NEB c.25510-17dupT variant involves the duplication of an intronic nucleotide 17 basepairs away from the exon-intron junction. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts no significant impact on ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in the large control database ExAC in 585 of 119984 control chromosomes (13 homozygotes) in all ethnicities, but was predominantly observed in the East Asian subpopulation at a frequency of 0.046692 (398/8524 [11 homozygotes]). This frequency is about 13 times the estimated maximal expected allele frequency of a pathogenic NEB variant (0.0035355), providing strong evidence that this is likely a benign polymorphism found primarily in the populations of East Asian origin. In addition, one clinical diagnostic laboratory has classified this variant as benign. To our knowledge, the variant of interest has not been reported in affected individuals via publications, nor has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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