ClinVar Miner

Submissions for variant NM_001048171.1(MUTYH):c.42C>T (p.Ile14=) (rs202240122)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212696 SCV000170419 benign not specified 2014-01-22 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 RCV000126888 SCV000213067 likely benign Hereditary cancer-predisposing syndrome 2014-08-09 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 RCV000204527 SCV000261164 likely benign MYH-associated polyposis 2020-12-07 criteria provided, single submitter clinical testing
Color Health, Inc RCV000126888 SCV000685627 likely benign Hereditary cancer-predisposing syndrome 2016-11-29 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212696 SCV000697697 likely benign not specified 2019-08-29 criteria provided, single submitter clinical testing
Counsyl RCV000204527 SCV000792800 likely benign MYH-associated polyposis 2017-07-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000204527 SCV001257717 uncertain significance MYH-associated polyposis 2017-04-28 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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355457 SCV001550348 uncertain significance Carcinoma of colon no assertion criteria provided clinical testing The MUTYH p.Ile14= variant was identified in 1 of 658 proband chromosomes (frequency: 0.0015) from individuals or families with FAP (Aretz_2006). The variant was also identified in dbSNP (ID: rs202240122) as With Likely benign, Uncertain significance allele, and in ClinVar (classified as benign by GeneDx; as likely benign by Ambry Genetics, Invitae, Color Genomics). The variant was not identified in COGR or UMD-LSDB databases. The variant was identified in control databases in 25 of 277226 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 2 of 24032 chromosomes (freq: 0.0001), European in 23 of 126718 chromosomes (freq: 0.0002); it was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Ile14 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. However, 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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