ClinVar Miner

Submissions for variant NM_001352514.2(HLCS):c.*7_*9del (rs201681436)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000185947 SCV000238904 benign not specified 2014-04-02 criteria provided, single submitter clinical testing The variant is found in MITONUC-MITOP panel(s).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000185947 SCV001737831 benign not specified 2021-05-20 criteria provided, single submitter clinical testing Variant summary: HLCS c.*7_*9delGCG is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.0086 in 249008 control chromosomes in the gnomAD database, including 17 homozygotes. The observed variant frequency is approximately 3-fold of the estimated maximal expected allele frequency for a pathogenic variant in HLCS causing Holocarboxylase Synthetase Deficiency phenotype (0.0028), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.*7_*9delGCG in individuals affected with Holocarboxylase Synthetase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submitter (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Natera, Inc. RCV001273642 SCV001456934 benign Holocarboxylase synthetase deficiency 2020-09-16 no assertion criteria provided clinical testing

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