ClinVar Miner

Submissions for variant NM_000546.6(TP53):c.216C>T (p.Pro72=)

gnomAD frequency: 0.00022  dbSNP: rs56275308
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163616 SCV000214183 likely benign Hereditary cancer-predisposing syndrome 2014-07-14 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001081606 SCV000253308 likely benign Li-Fraumeni syndrome 2021-11-18 criteria provided, single submitter clinical testing
GeneDx RCV000444926 SCV000516188 benign not specified 2015-04-30 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.
Color Diagnostics, LLC DBA Color Health RCV000163616 SCV000686728 likely benign Hereditary cancer-predisposing syndrome 2016-06-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589597 SCV000697437 benign not provided 2017-04-27 criteria provided, single submitter clinical testing Variant summary: The TP53 c.216C>T (p.Pro72Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 7/120822 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.000602 (6/9970). This frequency is about 15 times the estimated maximal expected allele frequency of a pathogenic TP53 variant (0.0000398), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Genetic Services Laboratory,University of Chicago RCV000444926 SCV002070803 likely benign not specified 2019-06-14 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000163616 SCV002530434 benign Hereditary cancer-predisposing syndrome 2021-11-26 criteria provided, single submitter curation
Genome-Nilou Lab RCV000163616 SCV002582276 likely benign Hereditary cancer-predisposing syndrome 2022-06-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002288721 SCV002582938 likely benign Li-Fraumeni syndrome 1 2022-06-18 criteria provided, single submitter clinical testing

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