ClinVar Miner

Submissions for variant NM_000038.6(APC):c.4456_4458del (p.Asp1486del)

dbSNP: rs761504791
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410631 SCV000487781 uncertain significance Familial adenomatous polyposis 1 2015-11-21 criteria provided, single submitter clinical testing
Invitae RCV003650577 SCV000552780 uncertain significance Familial adenomatous polyposis 1 2024-01-21 criteria provided, single submitter clinical testing This variant, c.4456_4458del, results in the deletion of 1 amino acid(s) of the APC protein (p.Asp1486del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs761504791, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 371788). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Color Diagnostics, LLC DBA Color Health RCV000580184 SCV000681667 uncertain significance Hereditary cancer-predisposing syndrome 2023-12-05 criteria provided, single submitter clinical testing This variant is a single amino acid deletion at position 1486 in the APC protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with APC-related disorders in the literature. This variant has been identified in 2/250820 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000580184 SCV001184255 uncertain significance Hereditary cancer-predisposing syndrome 2020-11-30 criteria provided, single submitter clinical testing The c.4456_4458delGAT variant (also known as p.D1486del) is located in coding exon 15 of the APC gene. This variant results from an in-frame GAT deletion at nucleotide positions 4456 to 4458. This results in the in-frame deletion of an aspartic acid at codon 1486. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV001545855 SCV001765265 uncertain significance not provided 2019-10-24 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at a significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 16753179)
Myriad Genetics, Inc. RCV000410631 SCV004018441 uncertain significance Familial adenomatous polyposis 1 2023-02-14 criteria provided, single submitter clinical testing This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.
Baylor Genetics RCV000410631 SCV004198181 uncertain significance Familial adenomatous polyposis 1 2023-09-21 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001545855 SCV004219427 uncertain significance not provided 2022-12-28 criteria provided, single submitter clinical testing To the best of our knowledge, the variant has not been reported in the published literature. The frequency of this variant in the general population, 0.000008 (2/250820 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Based on the available information, we are unable to determine the clinical significance of this variant.

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