NM_000546.6(TP53):c.97-5T>G AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 4, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004015314.2

Allele description [Variation Report for NM_000546.6(TP53):c.97-5T>G]

NM_000546.6(TP53):c.97-5T>G

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.97-5T>G

HGVS:

NC_000017.11:g.7676277A>C
NG_017013.2:g.16274T>G
NM_000546.6:c.97-5T>GMANE SELECT
NM_001126112.3:c.97-5T>G
NM_001126113.3:c.97-5T>G
NM_001126114.3:c.97-5T>G
NM_001126118.2:c.-21-5T>G
NM_001276695.3:c.-21-5T>G
NM_001276696.3:c.-21-5T>G
NM_001276760.3:c.-21-5T>G
NM_001276761.3:c.-21-5T>G
NM_001407262.1:c.97-5T>G
NM_001407263.1:c.-21-5T>G
NM_001407264.1:c.97-5T>G
NM_001407265.1:c.-21-5T>G
NM_001407266.1:c.97-5T>G
NM_001407267.1:c.-21-5T>G
NM_001407268.1:c.97-5T>G
NM_001407269.1:c.-21-5T>G
NM_001407270.1:c.97-5T>G
NM_001407271.1:c.-21-5T>G
LRG_321:g.16274T>G
NC_000017.10:g.7579595A>C

Molecular consequence:

NM_000546.6:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001126118.2:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001276696.3:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407262.1:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407263.1:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407264.1:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407265.1:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407266.1:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407267.1:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407268.1:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407269.1:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407270.1:c.97-5T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407271.1:c.-21-5T>G - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Li-Fraumeni syndrome (LFS)
Synonyms:: Sarcoma family syndrome of Li and Fraumeni
Identifiers:: MONDO: MONDO:0018875; MedGen: C0085390; OMIM: PS151623

Recent activity

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Homo sapiens coagulation factor VIII (F8), RefSeqGene (LRG_555) on chromosome X
Homo sapiens coagulation factor VIII (F8), RefSeqGene (LRG_555) on chromosome X
gi|1955884805|ref|NG_011403.2||gnl| RG_555

Nucleotide
FAM223A family with sequence similarity 223 member A [Homo sapiens]
FAM223A family with sequence similarity 223 member A [Homo sapiens]
Gene ID:100132967

Gene
LOC130068870 [Homo sapiens]
LOC130068870 [Homo sapiens]
Gene ID:130068870

Gene
MIR1184-3 microRNA 1184-3 [Homo sapiens]
MIR1184-3 microRNA 1184-3 [Homo sapiens]
Gene ID:100422977

Gene
SNORA36A small nucleolar RNA, H/ACA box 36A [Homo sapiens]
SNORA36A small nucleolar RNA, H/ACA box 36A [Homo sapiens]
Gene ID:677817

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004830449	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Sep 4, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004830449

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Sep 4, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004830449.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

This variant causes a T to G nucleotide substitution at the -5 position of intron 3 of the TP53 gene. 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 been identified in 1/250742 chromosomes 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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