ClinVar Miner

Submissions for variant NM_001048171.1(MUTYH):c.942C>T (p.Asp314=) (rs587780752)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000123159 SCV000166464 likely benign MYH-associated polyposis 2020-12-02 criteria provided, single submitter clinical testing
Counsyl RCV000123159 SCV000487357 likely benign MYH-associated polyposis 2016-05-25 criteria provided, single submitter clinical testing
GeneDx RCV000441650 SCV000525024 likely benign not specified 2018-03-12 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 RCV000567348 SCV000666455 likely benign Hereditary cancer-predisposing syndrome 2015-10-11 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Color Health, Inc RCV000567348 SCV000685683 likely benign Hereditary cancer-predisposing syndrome 2017-04-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000757499 SCV000885749 likely benign not provided 2018-03-17 criteria provided, single submitter clinical testing The c.984C>T; p.Asp328Asp variant (rs587780752, ClinVar variant ID 135993) does not alter the amino acid sequence of the MUTYH protein and computational splice site prediction algorithms do not predict a change in the nearest splice site or creation of a cryptic splice site. This variant has not been reported in medical literature or in gene specific variation databases. This variant is listed in the genome Aggregation Database (gnomAD) with an overall population frequency of 0.001% (identified on 4 out of 277,162 chromosomes). Based on the available information, the c.984C>T variant is likely to be benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000441650 SCV001363479 likely benign not specified 2020-01-31 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000123159 SCV001551753 likely benign MYH-associated polyposis no assertion criteria provided clinical testing The MUTYH p.Asp328= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, or UMD-LSDB databases. The variant was identified in dbSNP (ID: rs587780752) as "With Likely benign, Uncertain significance allele", and in ClinVar (classified as likely benign by Invitae, Counsyl, GeneDx, Ambry Genetics and Color Genomics). The variant was identified in control databases in 4 of 277162 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 2 of 126666 chromosomes (freq: 0.00002), and South Asian in 2 of 30782 chromosomes (freq: 0.00007); it was not observed in the African, Other, Latino, Ashkenazi Jewish, East Asian, and Finnish, populations. The p.Asp328 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. The variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. 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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