ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3006C>T (p.Ala1002=) (rs72541810)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000211905 SCV000209477 benign not specified 2014-08-26 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 RCV000159520 SCV000213108 likely benign Hereditary cancer-predisposing syndrome 2014-08-15 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 RCV000205109 SCV000260133 likely benign Familial adenomatous polyposis 1 2020-12-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000211905 SCV000600072 benign not specified 2017-07-19 criteria provided, single submitter clinical testing
Color Health, Inc RCV000159520 SCV000681570 likely benign Hereditary cancer-predisposing syndrome 2016-05-03 criteria provided, single submitter clinical testing
Counsyl RCV000205109 SCV000785986 likely benign Familial adenomatous polyposis 1 2018-01-26 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000858104 SCV001154461 likely benign not provided 2018-08-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001253906 SCV001429787 likely benign APC-Associated Polyposis Disorders 2019-02-13 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001287010 SCV001473648 likely benign none provided 2019-10-16 criteria provided, single submitter clinical testing
True Health Diagnostics RCV000159520 SCV000787834 likely benign Hereditary cancer-predisposing syndrome 2017-12-01 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356478 SCV001551659 likely benign Carcinoma of colon no assertion criteria provided clinical testing The APC p.Ala1002= variant was not identified in the literature, but was identified in dbSNP (ID: rs72541810) as “Likely Benign”, ClinVar database (3 submissions: 1x Benign by GeneDx, 2x Likely Benign by Ambry Genetics & Invitae), COSMIC (Adenocarcinoma of the large intestine), LOVD Zhejiang Colon Cancer Database (LOVD) (unknown), Clinvitae database (as 2x Likely Benign and 1x Benign). This variant was also identified in the NHLBI GO Exome Sequencing Project in 3 of 8600 European American alleles (Freq: 0.00034) and the Exome Aggregation Consortium database (August 8th 2016) in 21 of 121266 chromosomes (freq. 0.000217) in the following populations: European (Non-Finnish) in 20 of 66618 chromosomes (freq. 0.0003), Latino in 1 of 11574 chromosomes (freq. 8.4 x 10 -5), but was not seen in African, East Asian, Finnish, other and South Asian populations. This variant was not identified in the InSiGHT Colon Cancer Gene Variant Database (LOVD), GeneInsight - COGR, UMD and the 1000 Genome Project database. In addition this variant was identified by our laboratory in a patient with MAP as co-occurring with pathogenic MUTYH homozygous variants (p.Tyr179Cys) increasing the likelihood that the p.Ala1002+ variant does not have clinical significance. The p.Ala1002= 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.

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