ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.1573C>G (p.Pro525Ala) (rs73346297)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000123800 SCV000167143 benign not specified 2013-12-02 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000461945 SCV000559497 benign Oligodontia-colorectal cancer syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV001012214 SCV001172640 benign Hereditary cancer-predisposing syndrome 2018-09-20 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
Integrated Genetics/Laboratory Corporation of America RCV000123800 SCV001362151 benign not specified 2019-01-15 criteria provided, single submitter clinical testing Variant summary: AXIN2 c.1573C>G (p.Pro525Ala) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0026 in 277090 control chromosomes in the gnomAD database, including 14 homozygotes. The observed variant frequency is approximately 19-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in AXIN2 causing Colorectal Cancer phenotype (0.00014), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1573C>G in individuals affected with Colorectal Cancer and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000123800 SCV000691783 likely benign not specified no assertion criteria provided clinical testing

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