ClinVar Miner

Submissions for variant NM_000038.6(APC):c.1005A>G (p.Leu335=) (rs3797704)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723617 SCV000109809 uncertain significance not provided 2013-04-19 criteria provided, single submitter clinical testing
Invitae RCV000723617 SCV000166011 benign not provided 2019-03-02 criteria provided, single submitter clinical testing
GeneDx RCV000077980 SCV000512061 benign not specified 2015-07-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000491005 SCV000579801 likely benign Hereditary cancer-predisposing syndrome 2015-11-24 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000077980 SCV000591062 likely benign not specified 2012-07-17 criteria provided, single submitter clinical testing
Color RCV000491005 SCV000681439 benign Hereditary cancer-predisposing syndrome 2016-03-17 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000077980 SCV000916488 benign not specified 2017-12-11 criteria provided, single submitter clinical testing Variant summary: The APC c.1005A>G (p.Leu335Leu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts the creation of SRp40 binding site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 41/276982 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.001962 (37/18854). This frequency is about 27 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. This variant was reported in one breast patient but also in controls (Chang_2016) and also as a somatic occurrence (Chang_2016). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. Taken together, this variant is classified as benign.

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