ClinVar Miner

Submissions for variant NM_000053.4(ATP7B):c.3891C>T (p.Val1297=) (rs114771537)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589297 SCV000883439 benign not provided 2017-08-22 criteria provided, single submitter clinical testing
GeneDx RCV000145279 SCV000521846 benign not specified 2016-12-12 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.
Genetic Services Laboratory, University of Chicago RCV000145279 SCV000192354 benign not specified 2014-05-23 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000384354 SCV000384647 uncertain significance Wilson disease 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589297 SCV000694457 benign not provided 2017-02-03 criteria provided, single submitter clinical testing Variant summary: The ATP7B c.3891C>T (p.Val1297Val) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict the strenghtening of a canonical splice acceptor site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 348/120764 control chromosomes (3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.032967 (324/9828). This frequency is about 6 times the estimated maximal expected allele frequency of a pathogenic ATP7B variant (0.0054006), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likley benign. 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. Taken together, due to the synonymous nature of the variant, the lack of predicted detrimental effect on splicing, and the relatively high frequency in the population, this variant is classified as benign.
Invitae RCV000384354 SCV000626860 benign Wilson disease 2017-12-05 criteria provided, single submitter clinical testing
PreventionGenetics RCV000145279 SCV000301722 likely benign not specified criteria provided, single submitter clinical testing

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