ClinVar Miner

Submissions for variant NM_004360.5(CDH1):c.48+15_48+16del

gnomAD frequency: 0.00006  dbSNP: rs730881655
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000160370 SCV000210879 benign Hereditary cancer-predisposing syndrome 2013-10-30 criteria provided, single submitter clinical testing The variant is found in BR-OV-HEREDIC,HIRISK-BR-HEREDIC panel(s).
Counsyl RCV000411912 SCV000489013 likely benign Hereditary diffuse gastric adenocarcinoma 2016-08-01 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000160370 SCV000684461 likely benign Hereditary cancer-predisposing syndrome 2016-01-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000411912 SCV002349831 likely benign Hereditary diffuse gastric adenocarcinoma 2025-01-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002505193 SCV002798116 likely benign Familial cancer of breast; Blepharocheilodontic syndrome 1; Endometrial carcinoma; Hereditary diffuse gastric adenocarcinoma; Ovarian neoplasm; Malignant tumor of prostate 2022-03-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354450 SCV001549068 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The CDH1 c.48+15_48+16del variant was not identified in the literature nor was it identified in the Zhejiang University database. The variant was identified in dbSNP (ID: rs730881655) as "With Likely benign allele", and in ClinVar (classified as benign by GeneDx; as likely benign by Counsyl, Color Genomics). The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) 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 although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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