ClinVar Miner

Submissions for variant NM_000038.6(APC):c.3209A>T (p.Asn1070Ile)

dbSNP: rs1315959337
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000567455 SCV000667274 uncertain significance Hereditary cancer-predisposing syndrome 2016-09-08 criteria provided, single submitter clinical testing The p.N1070I variant (also known as c.3209A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide position 3209. The asparagine at codon 1070 is replaced by isoleucine, an amino acid with dissimilar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6502 samples (13004 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.003% (greater than 90000 alleles tested) in our clinical cohort. This amino acid position is poorly 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.
Invitae RCV003767132 SCV002123312 uncertain significance Familial adenomatous polyposis 1 2021-05-28 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 482241). This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with isoleucine at codon 1070 of the APC protein (p.Asn1070Ile). The asparagine residue is weakly conserved and there is a large physicochemical difference between asparagine and isoleucine.

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