ClinVar Miner

Submissions for variant NM_002354.3(EPCAM):c.344_345inv (p.Met115Thr)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002274939 SCV000252770 benign not provided 2023-11-06 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000780224 SCV000917318 benign not specified 2017-09-19 criteria provided, single submitter clinical testing Variant summary: The EPCAM c.344_345delinsCA (p.Met115Thr) variant causes a missense change involving a codon located in the Thyroglobulin type-1 domain (InterPro). Four in silico tools predicted a benign outcome for this variant. This variant was found in 3/246238 control chromosomes from all ethnicities at a frequency of 0.0000122, which does not exceed the estimated maximal expected allele frequency of a pathogenic EPCAM variant (0.0000284). However, two subpopulations (Latino and South Asian) have frequencies that do exceed this maximum, suggesting the variant may be a benign polymorphism in these populations. In addition, the EPCAM c.344C>T variant (classified as benign in our internal database) causes the same p.Met115Thr change and is reported as the predominant allele in the gnomAD database with a frequency of 0.5225 (144772/277076 chromosomes, 40945 homozygotes), strongly suggesting this is a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Due to the gnomAD frequency for the missense change, which the variant of interest also causes, this variant is classified as benign.
CeGaT Center for Human Genetics Tuebingen RCV002274939 SCV002563565 benign not provided 2022-07-01 criteria provided, single submitter clinical testing EPCAM: BS1, BS2
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003316098 SCV004017465 benign Lynch syndrome 8 2023-07-07 criteria provided, single submitter clinical testing

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