ClinVar Miner

Submissions for variant NM_000038.6(APC):c.7504G>A (p.Gly2502Ser) (rs2229995)

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Total submissions: 17
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000077994 SCV000109831 benign not specified 2012-08-22 criteria provided, single submitter clinical testing
Invitae RCV001079292 SCV000153849 benign Familial adenomatous polyposis 1 2020-11-28 criteria provided, single submitter clinical testing
GeneDx RCV000077994 SCV000167015 benign not specified 2013-10-14 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.
Ambry Genetics RCV000157722 SCV000212882 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000239067 SCV000297025 benign Familial multiple polyposis syndrome 2015-08-07 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000077994 SCV000301605 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000307201 SCV000452046 benign APC-Associated Polyposis Disorders 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Color Health, Inc RCV000157722 SCV000537375 benign Hereditary cancer-predisposing syndrome 2015-03-27 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001283365 SCV001156605 benign none provided 2020-07-10 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034399 SCV000043139 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
ITMI RCV000077994 SCV000084177 not provided not specified 2013-09-19 no assertion provided reference population
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353410 SCV000591209 benign Carcinoma of colon no assertion criteria provided clinical testing The p.Gly2502Ser variant was previously identified in the literature in 138 of 6866 proband chromosomes (frequency 0.020) from individuals with adenoma or colorectal cancer and in 157 of 8192 control chromosomes (frequency 0.019) from healthy individuals (Cleary 2008, Hadjisavvas 2006, Miyoshi 1992, Scott 2004, Tranah 2005, Wong 2010, Zhou 2004). This variant was also identified in the dbSNP (ID#rs2229995), HGMD, and LOVD databases, and was reported in several populations including the ESP Project with a frequency of 0.020 in European American alleles, the 1000 Genomes Project with a frequency of 0.010, and HapMap-CEU with a frequency of 0.032. The p.Gly2502 residue is not conserved through evolution and the variant (Ser) is found at this position in chicken and fruitfly, increasing the likelihood that this is a benign variant. In addition, Tranah (2005) found that this variant was not associated with risk of colorectal cancer or adenoma in men and women, and Zhou (2004) did not observe segregation of this variant with disease. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000077994 SCV000691766 benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000157722 SCV000693490 benign Hereditary cancer-predisposing syndrome 2017-10-10 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000077994 SCV001798965 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000077994 SCV001807757 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000077994 SCV001958192 benign not specified no assertion criteria provided clinical testing

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