ClinVar Miner

Submissions for variant NM_000478.6(ALPL):c.534C>T (p.Tyr178=) (rs201250289)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000266690 SCV000354300 benign Hypophosphatasia 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000756986 SCV000884997 likely benign not provided 2018-03-04 criteria provided, single submitter clinical testing The c.534C>T; p.Tyr178Tyr variant (rs201250289) does not alter the amino acid sequence of the ALPL protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an East Asian population frequency of 0.47% (identified on 88 out of 18,866 chromosomes, including one homozygote), and is classified as likely benign in ClinVar (ID: 295544). Based on the available information, the c.534C>T variant is likely to be benign.
Invitae RCV000756986 SCV001048666 benign not provided 2020-12-07 criteria provided, single submitter clinical testing

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