ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.1485C>T (p.Gly495=) (rs770556906)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000456262 SCV000548614 uncertain significance Oligodontia-colorectal cancer syndrome 2020-01-07 criteria provided, single submitter clinical testing This sequence change affects codon 495 of the AXIN2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the AXIN2 protein. This variant is present in population databases (rs770556906, ExAC 0.01%). This variant has not been reported in the literature in individuals with AXIN2-related disease. ClinVar contains an entry for this variant (Variation ID: 408808). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV000608075 SCV000730138 likely benign not specified 2018-02-26 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.
Illumina Clinical Services Laboratory,Illumina RCV000456262 SCV001287225 likely benign Oligodontia-colorectal cancer syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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