ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3015C>T (p.Asn1005=) (rs74085888)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000252488 SCV000301711 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000252488 SCV000517796 likely benign not specified 2017-04-04 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000252488 SCV000602604 benign not specified 2016-12-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000252488 SCV000694435 benign not specified 2017-07-06 criteria provided, single submitter clinical testing Variant summary: The c.3015C>T (p.Asn1005=) in ATP7B gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.0020 (123/60690 chrs tested), predominantly in individuals of African origin (0.02; 110/5328 chrs, including 2 homozygous occurrences). The observed frequency exceeds the maximum expected allele frequency for a pathogenic variant in this gene (0.0054), suggesting that it is a benign polymorphism. The variant was identified in at least 1 HBOC pt without strong evidence for causality. The variant of interest has not, to our knowledge, been identified in affected individuals via published reports, but is cited as Benign/Likely Benign by reputable database/clinical laboratories. Taken together, based on the prevalence in general population the variant was classified as Benign.
Invitae RCV000631255 SCV000752281 benign Wilson disease 2020-12-07 criteria provided, single submitter clinical testing

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