ClinVar Miner

Submissions for variant NM_033056.4(PCDH15):c.55T>G (p.Ser19Ala) (rs11004439)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000039763 SCV000063452 benign not specified 2009-06-23 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000039763 SCV000315072 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000266605 SCV000363254 likely benign Nonsyndromic Hearing Loss, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000321670 SCV000363255 benign Usher syndrome type 1 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Integrated Genetics/Laboratory Corporation of America RCV000586437 SCV000699762 benign not provided 2016-04-25 criteria provided, single submitter clinical testing Variant summary: The PCDH15 c.55T>G variant affects a non-conserved nucleotide, resulting in amino acid change from Ser to Ala. 3/4 in-silico tools predict benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 25808/118352 control chromosomes (3055 homozygotes) at a frequency of 0.2180614, which is about 69 times of the maximal expected frequency of a pathogenic PCDH15 allele (0.0031623), suggesting this variant is a benign polymorphism. This variant is reported in USH patients without evidence for causality and authors listed the variant as a frequent SNP. In addition, one reputable clinical laboratory via ClinVar classified this variant as benign. Taken together, this variant was classified as Benign.

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