ClinVar Miner

Submissions for variant NM_001005242.3(PKP2):c.1539C>T (p.Asn513=) (rs535581825)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000156794 SCV000206515 likely benign not specified 2014-09-24 criteria provided, single submitter clinical testing p.Asn557Asn in exon 7 of PKP2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 0.3% (57/16512) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs535581825).
Illumina Clinical Services Laboratory,Illumina RCV000463611 SCV000378452 likely benign Arrhythmogenic right ventricular cardiomyopathy, type 9 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000156794 SCV000534149 likely benign not specified 2016-11-23 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.
Invitae RCV000463611 SCV000557327 benign Arrhythmogenic right ventricular cardiomyopathy, type 9 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588739 SCV000698464 benign not provided 2017-07-10 criteria provided, single submitter clinical testing Variant summary: The PKP2 c.1671C>T (p.Asn557Asn) 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 no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 60/121396 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.003452 (57/16512). This frequency is about 8 times the estimated maximal expected allele frequency of a pathogenic PKP2 variant (0.0004301), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/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, this variant is classified as benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000463611 SCV000743454 benign Arrhythmogenic right ventricular cardiomyopathy, type 9 2017-07-28 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000463611 SCV000744699 likely benign Arrhythmogenic right ventricular cardiomyopathy, type 9 2017-06-28 criteria provided, single submitter clinical testing
Color RCV000771815 SCV000904518 benign Cardiomyopathy 2018-10-08 criteria provided, single submitter clinical testing

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