ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.2272G>A (p.Ala758Thr)

gnomAD frequency: 0.00175  dbSNP: rs145007501
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000586946 SCV000149784 likely benign not provided 2021-03-01 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26406231, 21626677, 24581859, 25186949, 27090353, 25801821, 27365112, 29371908, 29772684)
Invitae RCV000205073 SCV000261931 benign Oligodontia-cancer predisposition syndrome 2021-12-18 criteria provided, single submitter clinical testing
Vantari Genetics RCV000115875 SCV000266997 uncertain significance Hereditary cancer-predisposing syndrome 2016-02-04 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000205073 SCV000405679 likely benign Oligodontia-cancer predisposition 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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586946 SCV000698520 likely benign not provided 2016-08-17 criteria provided, single submitter clinical testing Variant summary: The AXIN2 c.2272G>A (p.Ala758Thr) variant causes a missense change involving a non-conserved nucleotide with 3/4 in silico tools (SNPs&GO not captured due to low reliability index) predicting a benign outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 291/121600 (1/417), which exceeds the estimated maximal expected allele frequency for a pathogenic AXIN2 variant of 1/7037, suggesting this variant is likely a benign polymorphism. The variant of interest has been reported in an affected individual with tooth agenesis, but had no family history of colorectal cancer. However, tooth agenesis has been implicated as a precursor for cancer, although this cannot be established for the current variant due to limited available information. Multiple clinical laboratories cite the variant with conflicting classifications "uncertain significance" or "likely benign." Therefore, until additional information becomes available the variant of interest has been classified as Likely Benign.
Ambry Genetics RCV000115875 SCV001175793 likely benign Hereditary cancer-predisposing syndrome 2019-11-21 criteria provided, single submitter clinical testing Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign)
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000586946 SCV001473768 likely benign not provided 2021-02-17 criteria provided, single submitter clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV001762237 SCV002009783 uncertain significance Colorectal cancer 2021-11-03 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000212102 SCV002069068 benign not specified 2021-06-15 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000115875 SCV002537167 likely benign Hereditary cancer-predisposing syndrome 2021-07-30 criteria provided, single submitter curation
CSER _CC_NCGL, University of Washington RCV000417339 SCV000503519 likely benign Oligodontia; Colorectal cancer 2016-08-01 no assertion criteria provided research Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 19 year old with a history of a tubulovillous adenoma at age 16.
Mayo Clinic Laboratories,Mayo Clinic RCV000212102 SCV000691772 uncertain significance not specified no assertion criteria provided clinical testing
GenomeConnect, ClinGen RCV000586946 SCV000840120 not provided not provided no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000586946 SCV001970538 likely benign not provided no assertion criteria provided clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000212102 SCV002551230 uncertain significance not specified 2022-05-10 no assertion criteria provided clinical testing

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