ClinVar Miner

Submissions for variant NM_000546.5(TP53):c.18A>C (p.Ser6=) (rs573130482)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 9
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000213043 SCV000211771 benign not specified 2014-09-08 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 RCV000161041 SCV000214591 likely benign Hereditary cancer-predisposing syndrome 2014-10-20 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 RCV001079935 SCV000253307 likely benign Li-Fraumeni syndrome 2020-12-01 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000213043 SCV000602264 likely benign not specified 2017-05-17 criteria provided, single submitter clinical testing
Color Health, Inc RCV000161041 SCV000686724 likely benign Hereditary cancer-predisposing syndrome 2017-05-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000213043 SCV000697434 likely benign not specified 2020-08-21 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589460 SCV000888662 likely benign not provided 2017-05-17 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000213043 SCV000692103 likely benign not specified no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357147 SCV001552516 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The TP53 p.Ser6= variant was not identified in the literature nor was it identified in the COGR, LOVD 3.0, UMD-LSDB, or UMD TP53 Mutation, databases. The variant was identified in dbSNP (ID: rs573130482) as "With Uncertain significance, other allele", ClinVar (classified as benign by GeneDx; as likely benign by Ambry Genetics, Invitae and three other submitters; as uncertain significance by one submitter), and in IARC TP53 Database. The variant was identified in control databases in 3 of 245504 chromosomes at a frequency of 0.00001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the European in 3 of 111324 chromosomes (freq: 0.00003), while the variant was not observed in the African, Ashkenazi Jewish, East Asian, Finnish, Latino, Other, and South Asian populations. The p.Ser6= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.