ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3876G>A (p.Thr1292=)

gnomAD frequency: 0.00004  dbSNP: rs377494451
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001705547 SCV000512073 likely benign not provided 2019-08-28 criteria provided, single submitter clinical testing
Invitae RCV003766193 SCV000562583 likely benign Familial adenomatous polyposis 1 2023-12-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV000491341 SCV000579862 likely benign Hereditary cancer-predisposing syndrome 2015-09-25 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.
Color Diagnostics, LLC DBA Color Health RCV000491341 SCV000909265 likely benign Hereditary cancer-predisposing syndrome 2017-01-09 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000434349 SCV001774449 likely benign not specified 2021-07-17 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000434349 SCV000691744 likely benign not specified no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001357108 SCV001552460 likely benign Carcinoma of colon no assertion criteria provided clinical testing The APC p.Thr1292= variant was not identified in the literature nor was it identified in the LOVD 3.0 and UMD-LSDB databases. The variant was identified in dbSNP (rs377494451) as “with likely benign allele and ClinVar (classified as likely benign by Invitae, GeneDx, Ambry Genetics, Color and Mayo Clinic). The variant was identified in control databases in 4 of 276,740 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 24,028 chromosomes (freq: 0.00004), Other in 1 of 6456 chromosomes (freq: 0.0002), Latino in 1 of 34,390 chromosomes (freq: 0.00003), European in 1 of 126,310 chromosomes (freq: 0.000008); it was not observed in the Ashkenazi Jewish, East Asian, Finnish and South Asian populations. The p.Thr1292= 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 at a non-highly conserved nucleotide outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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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