ClinVar Miner

Submissions for variant NM_001126112.2(TP53):c.97-3C>T (rs786203749)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000167188 SCV000218025 uncertain significance Hereditary cancer-predisposing syndrome 2019-01-22 criteria provided, single submitter clinical testing Insufficient or conflicting evidence;In silico models in agreement (benign)
Invitae RCV000465475 SCV000545323 uncertain significance Li-Fraumeni syndrome 2019-09-13 criteria provided, single submitter clinical testing This sequence change falls in intron 3 of the TP53 gene. It does not directly change the encoded amino acid sequence of the TP53 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with TP53-related disease. ClinVar contains an entry for this variant (Variation ID: 187457). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. 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.
GeneDx RCV000478081 SCV000567393 uncertain significance not provided 2016-04-09 criteria provided, single submitter clinical testing This variant is denoted TP53 c.97-3C>T or IVS3-3C>T and consists of a C>T nucleotide substitution at the -3 position of intron 3 of the TP53 gene. This variant is not predicted to affect gene splicing. TP53 c.97-3C>T has not, to our knowledge, been published in the literature as pathogenic or benign. This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The cytosine (C) nucleotide that is altered is not conserved. Based on currently available information, it is unclear whether TP53 c.97-3C>T is pathogenic or benign. We consider it to be a variant of uncertain significance.
Color RCV000167188 SCV000691672 uncertain significance Hereditary cancer-predisposing syndrome 2019-10-22 criteria provided, single submitter clinical testing

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