ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.1009-13G>A

gnomAD frequency: 0.00001  dbSNP: rs557444760
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000581189 SCV000689425 likely benign Hereditary cancer-predisposing syndrome 2016-09-23 criteria provided, single submitter clinical testing
GeneDx RCV001704692 SCV000729099 likely benign not provided 2019-09-09 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek 2016)
Labcorp Genetics (formerly Invitae), Labcorp RCV001853915 SCV002237530 likely benign Hereditary diffuse gastric adenocarcinoma 2024-01-19 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV001853915 SCV005403945 likely benign Hereditary diffuse gastric adenocarcinoma 2024-09-17 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354785 SCV001549483 uncertain significance Malignant tumor of breast no assertion criteria provided clinical testing The CDH1 c.1009-13G>A variant was not identified in the literature. The variant was identified in dbSNP (ID: rs557444760) as "With Likely benign allele", and in ClinVar (classified as likely benign by Color and GeneDx). The variant was identified in control databases in 4 of 246244 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Latino in 1 of 33582 chromosomes (freq: 0.00003), East Asian in 2 of 17248 chromosomes (freq: 0.0001), and South Asian in 1 of 30778 chromosomes (freq: 0.00003), while the variant was not observed in the African, Other, European, Ashkenazi Jewish, and Finnish populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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