NM_000546.6(TP53):c.559+4del AND Li-Fraumeni syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 7, 2021
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:: RCV001957072.3

Allele description

NM_000546.6(TP53):c.559+4del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.559+4del

HGVS:

NC_000017.11:g.7675049del
NG_017013.2:g.17502del
NM_000546.6:c.559+4delMANE SELECT
NM_001126112.3:c.559+4del
NM_001126113.3:c.559+4del
NM_001126114.3:c.559+4del
NM_001126115.2:c.163+4del
NM_001126116.2:c.163+4del
NM_001126117.2:c.163+4del
NM_001126118.2:c.442+4del
NM_001276695.3:c.442+4del
NM_001276696.3:c.442+4del
NM_001276697.3:c.82+4del
NM_001276698.3:c.82+4del
NM_001276699.3:c.82+4del
NM_001276760.3:c.442+4del
NM_001276761.3:c.442+4del
LRG_321:g.17502del
NC_000017.10:g.7578367del

Links:

dbSNP: rs2151029682

NCBI 1000 Genomes Browser:

rs2151029682

Molecular consequence:

NM_000546.6:c.559+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.559+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.559+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.559+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126115.2:c.163+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126116.2:c.163+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126117.2:c.163+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126118.2:c.442+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.442+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276696.3:c.442+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276697.3:c.82+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276698.3:c.82+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276699.3:c.82+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.442+4del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.442+4del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002254432	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 7, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002254432

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 7, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002254432.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

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. Variants that disrupt 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 may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with TP53-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 5 of the TP53 gene. It does not directly change the encoded amino acid sequence of the TP53 protein. It affects a nucleotide within the consensus splice site.

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

Last Updated: Feb 20, 2024

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