ClinVar Miner

Submissions for variant NM_001039213.4(CEACAM16):c.565C>T (p.His189Tyr)

gnomAD frequency: 0.00005  dbSNP: rs370890913
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000825721 SCV000967171 likely benign not specified 2018-09-06 criteria provided, single submitter clinical testing The p.His189Tyr variant in CEACAM16 is classified as likely benign because it ha s been identified in 0.09% (11/12816) of East Asian chromosomes by the Genome Ag gregation Database (gnomAD, http://gnomad.broadinstitute.org). Computational pre diction tools and conservation analysis suggest that the p.His189Tyr variant may not impact the protein. ACMG/AMP Criteria applied: BS1, BP4.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001617 SCV001159068 uncertain significance Autosomal dominant nonsyndromic hearing loss 4B 2019-04-18 criteria provided, single submitter clinical testing The p.His189Tyr variant (rs370890913) has not been reported in the medical literature, is not listed in gene-specific variant databases, nor has it been previously identified in our laboratory. It is listed in the Exome Aggregation Consortium (ExAC) browser with an allele frequency in East Asian populations of 0.52% (identified in 5 out of 964 chromosomes) and the 1000 Genomes browser with an overall population frequency of greater than 1% in Bengali and Chinese populations. The histidine at codon 189 is moderately conserved considering 19 species (Alamut software v2.7.1), and computational analyses suggest this variant does not have a significant effect on CEACAM16 protein structure/function (SIFT: tolerated, PolyPhen2: benign, and Mutation Taster: polymorphism). However, the c.565C>T variant is also predicted to create a strong cryptic splice donor site within the coding region of exon 4 (Alamut software v2.7.1), although the exact impact of this variant on CEACAM16 mRNA processing cannot be precisely determined. Thus, based on the available information, the clinical significance of the c.565C>T; p.His189Tyr variant cannot be determined with certainty.
GeneDx RCV001544556 SCV001763711 likely benign not provided 2020-03-31 criteria provided, single submitter clinical testing
Invitae RCV001544556 SCV003445941 likely benign not provided 2023-12-22 criteria provided, single submitter clinical testing

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