ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3049_3051del (p.Asn1017del)

dbSNP: rs730881229
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000679054 SCV000209474 uncertain significance not provided 2023-04-11 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679054 SCV000600073 uncertain significance not provided 2020-03-20 criteria provided, single submitter clinical testing
Ambry Genetics RCV000569152 SCV000667240 uncertain significance Hereditary cancer-predisposing syndrome 2021-02-02 criteria provided, single submitter clinical testing The c.3049_3051delAAT variant (also known as p.N1017del) is located in coding exon 15 of the APC gene. This variant results from an in-frame AAT deletion at nucleotide positions 3049 to 3051. This results in the in-frame deletion of an asparagine at codon 1017. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (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.
Color Diagnostics, LLC DBA Color Health RCV000569152 SCV000681575 uncertain significance Hereditary cancer-predisposing syndrome 2023-08-10 criteria provided, single submitter clinical testing This variant causes an in-frame deletion of 1 amino acids at exon 16 of 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 1/251128 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.
Preventiongenetics, part of Exact Sciences RCV000679054 SCV000805387 uncertain significance not provided 2017-01-12 criteria provided, single submitter clinical testing
Invitae RCV003534397 SCV000836254 uncertain significance Familial adenomatous polyposis 1 2023-12-04 criteria provided, single submitter clinical testing This variant, c.3049_3051del, results in the deletion of 1 amino acid(s) of the APC protein (p.Asn1017del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs773578423, gnomAD 0.003%). 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: 181776). 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.

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