ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.1947-4C>T (rs74904335)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000440735 SCV000529873 likely benign not specified 2016-07-29 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 RCV000440735 SCV000918584 uncertain significance not specified 2017-10-05 criteria provided, single submitter clinical testing Variant summary: The ATP7B c.1947-4C>T variant causes a missense change involving the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 159/275932 control chromosomes including two homozygous occurrences (gnomAD), predominantly observed in the East Asian subpopulation at a frequency of 0.008075 (152/18824). This frequency is about 1.5 times the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006), suggesting this is possibly a benign rare polymorphism found primarily in the populations of East Asian origin. Two studies report this variant as a polymorphism, without clearly stating if it was found in WD patients or controls (Kim_1998, Kim_1998). One clinical diagnostic laboratory has classified this variant as likely benign. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV000631244 SCV000752268 benign Wilson disease 2017-09-11 criteria provided, single submitter clinical testing

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