ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3165A>T (p.Ile1055=) (rs61734287)

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Total submissions: 17
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000755211 SCV000153970 benign Familial adenomatous polyposis 1 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000211906 SCV000167004 benign not specified 2014-02-19 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 RCV000129160 SCV000183890 benign Hereditary cancer-predisposing syndrome 2014-11-24 criteria provided, single submitter clinical testing Does not segregate with disease in family study (genes with complete penetrance)
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000202973 SCV000257784 benign Familial multiple polyposis syndrome 2015-03-25 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000307559 SCV000452000 benign 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 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 RCV000211906 SCV000602504 benign not specified 2019-02-12 criteria provided, single submitter clinical testing
Color Health, Inc RCV000129160 SCV000681582 benign Hereditary cancer-predisposing syndrome 2016-03-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000211906 SCV000805388 benign not specified 2016-11-18 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV001529443 SCV001746824 likely benign not provided 2021-06-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353666 SCV000591131 benign Carcinoma of colon no assertion criteria provided clinical testing The APC, p.Ile1055Ile variant was not identified in the literature nor was it identified in the GeneInsight COGR through the Canadian Open Genetics Repository, CLINVITAE, COSMIC or MutDB databases. The variant was identified in dbSNP (ID: rs61734287 “With Benign allele”, with a minor allele frequency of 0.001(5 of 5000 in 1000 Genomes Project). In NHLBI Exome Sequencing Project (Exome Variant Server) the variant was identified in 34 of 8600 European Americans and 4 of 4405 African Americans. In the Exome Aggregation Consortium (ExAC) database (released Oct 20th, 2014), the variant was identified in 428 of 120724 chromosomes (frequency: 0.003545) (or 394 of 66424 alleles in the European (Non-Finnish) - 2 of them homozygous, 17 of 6610 alleles in the European (Finnish), 7 of 10258 of Africans, 6 of 11508 Latinos, 4 of 16456 South Asians), increasing the likelihood this could be a low frequency benign variant. The variant was also identified in the Clinvar database and classified as benign by Invitae, by Gene DX and by Ambry genetics; classified as neutral in UMD database and co-occurred with a pathogenic variant - APC: c.1248C>G, p.Tyr416X. It was identified 2X in InSiGHT Colon Cancer Database and 1X in Zhejiang Colon Cancer Database.The p.Ile1055Ile 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, this variant meets our laboratory's criteria to be classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000211906 SCV000691730 likely benign not specified no assertion criteria provided clinical testing
True Health Diagnostics RCV000129160 SCV000693475 likely benign Hereditary cancer-predisposing syndrome 2017-09-11 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV001529443 SCV001742912 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001529443 SCV001800609 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000211906 SCV001807284 benign not specified no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV001529443 SCV001922002 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV001529443 SCV001958003 likely benign not provided no assertion criteria provided clinical testing

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