ClinVar Miner

Submissions for variant NM_000546.6(TP53):c.97-3C>T

dbSNP: rs786203749
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen TP53 Variant Curation Expert Panel, ClinGen RCV001527082 SCV001737921 uncertain significance Li-Fraumeni syndrome 1 2021-04-02 reviewed by expert panel curation This variant is absent in the gnomAD cohort (PM2_Supporting; http://gnomad.broadinstitute.org). This variant has been observed in 2-7 60+ year old females without a cancer diagnosis (BS2_Supporting; internal laboratory contributor). In summary, the clinical significance of TP53 c.97-3C>T is uncertain for Li-Fraumeni syndrome. ACMG/AMP criteria applied, as specified by the TP53 Variant Curation Expert Panel: PM2_Supporting, BS2_Supporting.
Ambry Genetics RCV000167188 SCV000218025 likely benign Hereditary cancer-predisposing syndrome 2021-01-05 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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 RCV000465475 SCV000545323 likely benign Li-Fraumeni syndrome 2023-09-10 criteria provided, single submitter clinical testing
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 Diagnostics, LLC DBA Color Health RCV000167188 SCV000691672 uncertain significance Hereditary cancer-predisposing syndrome 2023-10-12 criteria provided, single submitter clinical testing This variant causes a C>T nucleotide substitution at the -3 position of intron 3 of the TP53 gene. Splice site prediction tools do not indicate that this variant may have a significant impact on RNA splicing. To our knowledge, RNA studies have not been reported for this variant. This variant has not been reported in individuals affected with TP53-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Sema4, Sema4 RCV000167188 SCV002532731 uncertain significance Hereditary cancer-predisposing syndrome 2021-12-05 criteria provided, single submitter curation
All of Us Research Program, National Institutes of Health RCV000465475 SCV004840071 uncertain significance Li-Fraumeni syndrome 2023-11-02 criteria provided, single submitter clinical testing This variant causes a C>T nucleotide substitution at the -3 position of intron 3 of the TP53 gene. Splice site prediction tools do not indicate that this variant may have a significant impact on RNA splicing. To our knowledge, RNA studies have not been reported for this variant. This variant has not been reported in individuals affected with TP53-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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