ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5026A>G (p.Arg1676Gly) (rs370560998)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000115100 SCV000213855 likely benign Hereditary cancer-predisposing syndrome 2017-05-04 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign),Other data supporting benign classification,Subpopulation frequency in support of benign classification
CSER_CC_NCGL; University of Washington Medical Center RCV000210376 SCV000190061 uncertain significance Familial multiple polyposis syndrome 2014-06-01 criteria provided, single submitter research Low GERP score may suggest that this variant belongs in a lower pathogenicity class
CSER_CC_NCGL; University of Washington Medical Center RCV000735965 SCV000864154 uncertain significance Colorectal cancer 2016-06-01 criteria provided, single submitter research Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 51 year old male diagnosed with colon cancer at age 50. Family history of colorectal cancer and/or polyps. Patient also has the APC c.7399C>A variant. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review.
Color RCV000115100 SCV000902642 likely benign Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000120016 SCV000591185 uncertain significance not specified 2016-08-12 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000120016 SCV000257786 uncertain significance not specified 2015-06-19 criteria provided, single submitter clinical testing
GeneDx RCV000120016 SCV000149009 likely benign not specified 2018-02-12 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.
ITMI RCV000120016 SCV000084146 not provided not specified 2013-09-19 no assertion provided reference population
Integrated Genetics/Laboratory Corporation of America RCV000587987 SCV000694067 uncertain significance not provided 2016-08-24 criteria provided, single submitter clinical testing Variant summary: Variant affects a non-conserved nucleotide and results in a replacement of a large size and basic Arginine (R) small size and hydrophobic Glycine (G). 3/4 in silico tools predict neutral outcome for this change (SNPs&GO was not considered due to low reliability index). Variant was found in the large and broad cohorts of the ExAC project at an allele frequency of 0.015% which exceeds the maximal expected allele frequency of a disease causing APC allele (0.006%). It was also found in one FAP patient and in one healthy control by Azzopardi_2008 and in one CRC patient (Kraus_2013) without strong evidence for pathogenicity. One functional study showed the variant to result in a slightly impaired ability to suppress beta-catenin regulated transcription (Azzopardi_2008); however it is unclear whether the level of this impaired CRT suppression ability is pathologically relevant. This variant was observed in a patient together with APC Pro2467Thr by our laboratory as well as by Azzopardi 2008, Kraus_2013 and in one individual listed in the UMD database; suggesting the two variant likely to be on the same chromosome (in cis). Considering all evidence, the variant is classified as a VUS-possibly benign.
Invitae RCV000148369 SCV000254020 likely benign Familial adenomatous polyposis 1 2018-01-08 criteria provided, single submitter clinical testing
Mendelics RCV000148369 SCV000838128 uncertain significance Familial adenomatous polyposis 1 2018-07-02 criteria provided, single submitter clinical testing
PreventionGenetics RCV000587987 SCV000805419 uncertain significance not provided 2017-06-01 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000115100 SCV000787837 likely benign Hereditary cancer-predisposing syndrome 2017-12-01 no assertion criteria provided clinical testing

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