NM_000546.6(TP53):c.516T>G (p.Val172=) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 26, 2017
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:: RCV000578979.1

Allele description [Variation Report for NM_000546.6(TP53):c.516T>G (p.Val172=)]

NM_000546.6(TP53):c.516T>G (p.Val172=)

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.516T>G (p.Val172=)

HGVS:

NC_000017.11:g.7675096A>C
NG_017013.2:g.17455T>G
NM_000546.6:c.516T>GMANE SELECT
NM_001126112.3:c.516T>G
NM_001126113.3:c.516T>G
NM_001126114.3:c.516T>G
NM_001126115.2:c.120T>G
NM_001126116.2:c.120T>G
NM_001126117.2:c.120T>G
NM_001126118.2:c.399T>G
NM_001276695.3:c.399T>G
NM_001276696.3:c.399T>G
NM_001276697.3:c.39T>G
NM_001276698.3:c.39T>G
NM_001276699.3:c.39T>G
NM_001276760.3:c.399T>G
NM_001276761.3:c.399T>G
NP_000537.3:p.Val172=
NP_000537.3:p.Val172=
NP_001119584.1:p.Val172=
NP_001119585.1:p.Val172=
NP_001119586.1:p.Val172=
NP_001119587.1:p.Val40=
NP_001119588.1:p.Val40=
NP_001119589.1:p.Val40=
NP_001119590.1:p.Val133=
NP_001263624.1:p.Val133=
NP_001263625.1:p.Val133=
NP_001263626.1:p.Val13=
NP_001263627.1:p.Val13=
NP_001263628.1:p.Val13=
NP_001263689.1:p.Val133=
NP_001263690.1:p.Val133=
LRG_321t1:c.516T>G
LRG_321:g.17455T>G
LRG_321p1:p.Val172=
NC_000017.10:g.7578414A>C
NM_000546.4:c.516T>G
NM_000546.5:c.516T>G

Links:

dbSNP: rs749309577

NCBI 1000 Genomes Browser:

rs749309577

Molecular consequence:

NM_000546.6:c.516T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.516T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.516T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.516T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126115.2:c.120T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126116.2:c.120T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126117.2:c.120T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.399T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276695.3:c.399T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276696.3:c.399T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276697.3:c.39T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276698.3:c.39T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276699.3:c.39T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.399T>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.399T>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000680591	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Sep 26, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680591

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Sep 26, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000680591.1

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

Description

This variant is denoted TP53 c.516T>G at the DNA level. Although this variant is silent at the codinglevel, preserving a Valine at codon 172, it is predicted to cause abnormal splicing through the creation of a new crypticsplice donor site upstream of the natural donor site. However, in the absence of RNA or functional studies, the actualeffect of this variant is unknown. While this variant has not, to our knowledge, been reported as a germline variant ithas been reported as a somatic variant in a neuroblastoma (Hosoi 1994). This variant was not observed in largepopulation cohorts (Lek 2016). The nucleotide which is altered, a thymine (T) at base 516, is not conserved. Based oncurrently available information, it is unclear whether TP53 c.516T>G is a pathogenic or benign variant. We consider itto be a variant of uncertain significance.

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

Last Updated: Sep 29, 2024

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