ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.1615G>A (p.Val539Met) (rs9913621)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212101 SCV000167144 benign not specified 2013-10-18 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.
Vantari Genetics RCV000123801 SCV000266998 benign Hereditary cancer-predisposing syndrome 2015-12-01 criteria provided, single submitter clinical testing
Invitae RCV000232669 SCV000288667 benign Oligodontia-colorectal cancer syndrome 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000232669 SCV000405691 likely benign Oligodontia-colorectal cancer syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Integrated Genetics/Laboratory Corporation of America RCV000587784 SCV000698515 benign not provided 2016-04-28 criteria provided, single submitter clinical testing Variant summary: The c.1615G>A variant affects a conserved nucleotide, resulting in amino acid change from Val to Met. 2/4 in-silico tools predict this variant to be benign (SNPs&GO not captured due to low reliability index). This variant is found in 491/121392 control chromosomes (14 homozygotes) at a frequency of 0.0040447, which is about 28 times of the maximal expected frequency of a pathogenic allele (0.0001421). Variant is predominalty observed in African subpopulation in ExAC with MAF of 0.0434365, suggesting this variant is benign especially in Africans. In addition, multiple clinical laboratories classified this variant as benign. Taken together, this variant was classified as benign.
Ambry Genetics RCV000123801 SCV001172874 benign Hereditary cancer-predisposing syndrome 2019-05-08 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
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000212101 SCV000691782 benign not specified no assertion criteria provided clinical testing

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