ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4326T>A (p.Pro1442=) (rs67622085)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001081086 SCV000153860 benign Familial adenomatous polyposis 1 2020-12-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV000131961 SCV000187018 benign Hereditary cancer-predisposing syndrome 2014-11-18 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
PreventionGenetics,PreventionGenetics RCV000254138 SCV000301594 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000361337 SCV000452010 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001283362 SCV000602525 benign none provided 2020-04-01 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000512763 SCV000609170 likely benign not provided 2017-05-01 criteria provided, single submitter clinical testing
Color Health, Inc RCV000131961 SCV000681660 benign Hereditary cancer-predisposing syndrome 2016-03-17 criteria provided, single submitter clinical testing
GeneDx RCV000512763 SCV001897989 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353752 SCV000591167 benign Carcinoma of colon no assertion criteria provided clinical testing The Pro1442Pro variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located near a splice junction, is listed in dbSNP (rs67622085) from a clinical source with an average heterozygosity and standard error of 0.018 +/- 0.093, and a global minor allele frequency (MAF) of 0.006 (1000 Genomes). It has not been previously identified by our laboratory among the 973 individuals who have undergone APC testing, but has been reported in the literature in 5/528 proband chromosomes (frequency 0.009) from individuals with colorectal cancer and sporadic ependymomas. It was found at higher frequencies in the 4/282 control chromosomes (frequency 0.014), increasing the likelihood that this is a benign variant (Onilude_2006_16843107, Worm_2004_15133491, Zhou_2004_15122587). In summary, based on the above information, the p.Pro1442ro variant is classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000254138 SCV000691748 likely benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000131961 SCV000693482 benign Hereditary cancer-predisposing syndrome 2017-09-28 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000254138 SCV001799289 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000254138 SCV001809111 benign not specified no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000254138 SCV001922838 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000254138 SCV001960148 benign not specified no assertion criteria provided clinical testing

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