ClinVar Miner

Submissions for variant NM_000038.6(APC):c.5250C>T (p.Val1750=) (rs2229997)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163958 SCV000214556 likely benign Hereditary cancer-predisposing syndrome 2014-12-18 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 RCV000200153 SCV000252928 benign Familial adenomatous polyposis 1 2020-12-04 criteria provided, single submitter clinical testing
Counsyl RCV000200153 SCV000488420 likely benign Familial adenomatous polyposis 1 2016-03-23 criteria provided, single submitter clinical testing
Color Health, Inc RCV000163958 SCV000681719 likely benign Hereditary cancer-predisposing syndrome 2016-10-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000859105 SCV001133346 benign not provided 2019-01-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001174930 SCV001338373 likely benign not specified 2020-02-21 criteria provided, single submitter clinical testing
GeneDx RCV000859105 SCV001875418 benign not provided 2015-05-12 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000859105 SCV001549884 likely benign not provided no assertion criteria provided clinical testing The APC p.Val1750= variant was not identified in the literature nor was it identified in the following databases: MutDB, UMD-LSDB, Zhejiang Colon Cancer Database. The variant was identified in dbSNP (ID: rs2229997) as “With Likely benign allele”, ClinVar (as likely benign by Ambry Genetics, Invitae, Counsyl, and Color Genomics), Clinvitae (2x), Cosmic (in a tumour in the large intestine), and LOVD 3.0 (1x). The variant was identified in control databases in 13 of 245396 chromosomes at a frequency of 0.000053 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: European (Non-Finnish) in 1 of 111010 chromosomes (freq: 0.000009), and Ashkenazi Jewish in 12 of 9812 chromosomes (freq: 0.001223); it was not observed in the African, Other, Latino, East Asian, European (Finnish), and South Asian populations. The p.Val1750= 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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