ClinVar Miner

Submissions for variant NM_000038.6(APC):c.8378G>A (p.Ser2793Asn)

gnomAD frequency: 0.00001  dbSNP: rs374853436
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679091 SCV000600166 uncertain significance not provided 2018-11-21 criteria provided, single submitter clinical testing
Invitae RCV003766871 SCV000647770 uncertain significance Familial adenomatous polyposis 1 2023-06-16 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt APC protein function. ClinVar contains an entry for this variant (Variation ID: 438891). This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 2793 of the APC protein (p.Ser2793Asn).
Ambry Genetics RCV000573141 SCV000667338 uncertain significance Hereditary cancer-predisposing syndrome 2021-10-21 criteria provided, single submitter clinical testing The p.S2793N variant (also known as c.8378G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 8378. The serine at codon 2793 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV000679091 SCV000805480 uncertain significance not provided 2017-11-10 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000573141 SCV000909640 uncertain significance Hereditary cancer-predisposing syndrome 2023-11-15 criteria provided, single submitter clinical testing This missense variant replaces serine with asparagine at codon 2793 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). 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 not been identified 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.
Genetic Services Laboratory, University of Chicago RCV001821420 SCV002066678 uncertain significance not specified 2020-11-05 criteria provided, single submitter clinical testing DNA sequence analysis of the APC gene demonstrated a sequence change, c.8378G>A, in exon 16 that results in an amino acid change, p.Ser2793Asn. This sequence change does not appear to have been previously described in patients with APC-related disorders and has also not been described in population databases (gnomAD, ExAC). The p.Ser2793Asn change affects a highly conserved amino acid residue located in a domain of the APC protein that is known to be functional. The p.Ser2793Asn substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Ser2793Asn change remains unknown at this time.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001821420 SCV004039027 uncertain significance not specified 2023-08-11 criteria provided, single submitter clinical testing

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