NM_000546.6(TP53):c.74+7_74+8del AND Li-Fraumeni syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Aug 8, 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:: RCV003509445.2

Allele description [Variation Report for NM_000546.6(TP53):c.74+7_74+8del]

NM_000546.6(TP53):c.74+7_74+8del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.74+7_74+8del

HGVS:

NC_000017.11:g.7676513_7676514del
NG_017013.2:g.16037_16038del
NM_000546.6:c.74+7_74+8delMANE SELECT
NM_001126112.3:c.74+7_74+8del
NM_001126113.3:c.74+7_74+8del
NM_001126114.3:c.74+7_74+8del
NM_001126118.2:c.-154_-153del
NM_001276695.3:c.-44+7_-44+8del
NM_001276696.3:c.-44+7_-44+8del
NM_001276760.3:c.-44+7_-44+8del
NM_001276761.3:c.-44+7_-44+8del
NM_001407262.1:c.74+7_74+8del
NM_001407263.1:c.-44+7_-44+8del
NM_001407264.1:c.74+7_74+8del
NM_001407265.1:c.-44+7_-44+8del
NM_001407266.1:c.74+7_74+8del
NM_001407267.1:c.-44+7_-44+8del
NM_001407268.1:c.74+7_74+8del
NM_001407269.1:c.-44+7_-44+8del
NM_001407270.1:c.74+7_74+8del
NM_001407271.1:c.-44+7_-44+8del
LRG_321t8:c.-154_-153del
LRG_321:g.16037_16038del
NC_000017.10:g.7579831_7579832del
NM_001126118.1:c.-154_-153delGG

Molecular consequence:

NM_001126118.2:c.-154_-153del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276696.3:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407262.1:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407263.1:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407264.1:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407265.1:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407266.1:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407267.1:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407268.1:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407269.1:c.-44+7_-44+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407270.1:c.74+7_74+8del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407271.1:c.-44+7_-44+8del - 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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PREDICTED: 5'/3'-nucleotidase SurE [Cucumis melo]
PREDICTED: 5'/3'-nucleotidase SurE [Cucumis melo]
gi|659093628|ref|XP_008447629.1|

Protein
AT-hook motif nuclear-localized protein 23-like [Cucumis melo]
AT-hook motif nuclear-localized protein 23-like [Cucumis melo]
gi|659132002|ref|XP_008465963.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004312720	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 8, 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

SCV004312720

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 8, 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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004312720.1

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

#	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: Nov 10, 2024

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