ClinVar Miner

Submissions for variant NM_000546.5(TP53):c.102C>G (p.Pro34=) (rs11575998)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000165856 SCV000216605 likely benign Hereditary cancer-predisposing syndrome 2014-09-03 criteria provided, single submitter clinical testing
Color RCV000165856 SCV000686715 likely benign Hereditary cancer-predisposing syndrome 2016-07-28 criteria provided, single submitter clinical testing
GeneDx RCV000420887 SCV000514933 likely benign not specified 2018-01-02 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.
Integrated Genetics/Laboratory Corporation of America RCV000420887 SCV000918348 likely benign not specified 2018-08-31 criteria provided, single submitter clinical testing Variant summary: TP53 c.102C>G alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 3.3e-05 in 276916 control chromosomes, but was predominantly found within the Latino subpopulation in the gnomAD database at a frequency of 0.00015. This frequency is nearly 4-fold higher than the maximal expected allele frequency for a pathogenic variant in Li-Fraumeni Syndrome, suggesting the variant is a benign polymorphism in individuals of Latino origin. To our knowledge, no occurrence of c.102C>G in individuals affected with Li-Fraumeni Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV000527483 SCV000629766 likely benign Li-Fraumeni syndrome 2017-12-27 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000760099 SCV000889880 benign not provided 2018-03-06 criteria provided, single submitter clinical testing

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