ClinVar Miner

Submissions for variant NM_000038.6(APC):c.450A>G (p.Lys150=) (rs116020626)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000211893 SCV000209484 benign not specified 2014-08-29 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 RCV000159527 SCV000213274 likely benign Hereditary cancer-predisposing syndrome 2014-08-22 criteria provided, single submitter clinical testing This alteration is classified as likely 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.
Invitae RCV000199795 SCV000252922 likely benign Familial adenomatous polyposis 1 2020-12-07 criteria provided, single submitter clinical testing
Counsyl RCV000199795 SCV000488938 likely benign Familial adenomatous polyposis 1 2016-07-25 criteria provided, single submitter clinical testing
Color Health, Inc RCV000159527 SCV000681670 benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759433 SCV000888747 benign not provided 2019-01-24 criteria provided, single submitter clinical testing
Mendelics RCV000199795 SCV001136874 likely benign Familial adenomatous polyposis 1 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000759433 SCV001154454 likely benign not provided 2019-07-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001156933 SCV001318473 uncertain significance APC-Associated Polyposis Disorders 2018-01-12 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353868 SCV000591031 likely benign Carcinoma of colon no assertion criteria provided clinical testing The APC p.Lys150Lys variant was identified in 1 of 3082 proband chromosomes (frequency: 0.0003) from individuals or families being evaluated for FAP (Kerr 2013). The variant was also identified in dbSNP (ID: rs116020626) “With other allele”, Clinvitae database (with conflicting interpretations), InSiGHT Colon Cancer Gene Variant Database (LOVD), ClinVar database (classification benign by GeneDx, and likely benign by Ambry Genetics and Invitae), and UMD (2x with a “likely neutral” classification, and co-occurring with a pathogenic APC mutation, c.1312+3A>G). This variant was also identified in the 1000 Genomes Project in 2 of 5000 chromosomes (frequency: 0.0004); HAPMAP-EUR in 2 of 1006 chromosomes (frequency: 0.002); NHLBI GO Exome Sequencing Project (ESP) in 4 of 8582 European American alleles, and the Exome Aggregation Consortium (ExAC) database (released Jan 13, 2015) in 14 of 66536 chromosomes (frequency: 0.0002) from a population of European (Non-Finnish) individuals. The p.Lys150Lys variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
True Health Diagnostics RCV000159527 SCV000787836 likely benign Hereditary cancer-predisposing syndrome 2017-12-01 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000759433 SCV001740730 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000759433 SCV001807434 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000759433 SCV001925579 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000759433 SCV001957855 likely benign not provided no assertion criteria provided clinical testing

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