ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.1952C>T (p.Ser651Leu) (rs74006838)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000587836 SCV000149779 likely benign not provided 2021-06-05 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 28481359)
Invitae RCV001082227 SCV000288682 benign Oligodontia-colorectal cancer syndrome 2020-12-04 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587836 SCV000698518 benign not provided 2017-06-23 criteria provided, single submitter clinical testing Variant summary: The AXIN2 c.1952C>T (p.Ser651Leu) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant. This variant was found in 47/117962 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.004176 (40/9578). This frequency is about 29 times the estimated maximal expected allele frequency of a pathogenic AXIN2 variant (0.0001421), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. An internal LCA sample reports the variant to co-occur with two MUTYH pathogenic variants, c.536A>G and c.1187G>A. Taken together, this variant is classified as benign.
Ambry Genetics RCV001013820 SCV001174453 benign Hereditary cancer-predisposing syndrome 2019-01-03 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;In silico models in agreement (benign)
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001285112 SCV001471475 likely benign none provided 2020-01-24 criteria provided, single submitter clinical testing

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