ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3386T>C (p.Leu1129Ser) (rs143638171)

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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000077988 SCV000602522 benign not specified 2016-07-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV000115083 SCV000185955 benign Hereditary cancer-predisposing syndrome 2014-08-11 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034384 SCV000043121 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000034384 SCV000610443 likely benign not provided 2017-03-20 criteria provided, single submitter clinical testing
Color RCV000115083 SCV000681596 benign Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000077988 SCV000591139 benign not specified 2015-07-09 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000203169 SCV000257785 uncertain significance Familial multiple polyposis syndrome 2015-04-14 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000077988 SCV000109820 benign not specified 2013-07-02 criteria provided, single submitter clinical testing
GeneDx RCV000077988 SCV000148992 likely benign not specified 2017-12-27 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 RCV000077988 SCV000084182 not provided not specified 2013-09-19 no assertion provided reference population
Illumina Clinical Services Laboratory,Illumina RCV000393833 SCV000452005 likely benign APC-Associated Polyposis Disorders 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000034384 SCV000694031 likely benign not provided 2016-09-02 criteria provided, single submitter clinical testing Variant summary: This c.3386T>C variant affects a conserved nucleotide, resulting in amino acid change from Leu to Ser. 2/3 in-silico tools used predict this variant to be damaging. This variant was found in 204/121934 control chromosomes including the broad and large populations from ExAC at a frequency of 0.001673, which is more than 27 times greater than the maximal expected frequency of a pathogenic allele (0.0000602) in this gene, suggesting this variant is benign. The variant particularly more common in European (Non-Finnish) population with allele frequency of 0.25% (171/66304 chromosomes) including two homozygotes. The variant has also been reported in cancer patients in literature, mainly of CRC and FAP patients, without strong evidence for causality. One reputable database (UMD) reports this variants co-occurrence in trans with complete APC gene deletion strongly suggesting for a benign outcome. In addition, the same database also reports finding of this variant in an unaffected relative, possibly suggesting a lack of cosegregation. In a small case-control study, this variant did not lead to an increased risk of CRC (Zhou_2004). Multiple clinical labs have classified this variant as benign/likely benign (4 labs) to uncertain significance (1 lab). Taken together, this variant has currently been classified as likely benign.
Invitae RCV000196915 SCV000252583 benign Familial adenomatous polyposis 1 2018-01-10 criteria provided, single submitter clinical testing
Mendelics RCV000196915 SCV000838106 likely benign Familial adenomatous polyposis 1 2018-07-02 criteria provided, single submitter clinical testing
PreventionGenetics RCV000077988 SCV000301592 benign not specified criteria provided, single submitter clinical testing
True Health Diagnostics RCV000115083 SCV000693477 likely benign Hereditary cancer-predisposing syndrome 2017-10-16 no assertion criteria provided clinical testing

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