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NM_000546.6(TP53):c.216C>T (p.Pro72=) AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
Apr 27, 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:
RCV000589597.5

Allele description [Variation Report for NM_000546.6(TP53):c.216C>T (p.Pro72=)]

NM_000546.6(TP53):c.216C>T (p.Pro72=)

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.216C>T (p.Pro72=)
HGVS:
  • NC_000017.11:g.7676153G>A
  • NG_017013.2:g.16398C>T
  • NM_000546.6:c.216C>TMANE SELECT
  • NM_001126112.3:c.216C>T
  • NM_001126113.3:c.216C>T
  • NM_001126114.3:c.216C>T
  • NM_001126118.2:c.99C>T
  • NM_001276695.3:c.99C>T
  • NM_001276696.3:c.99C>T
  • NM_001276760.3:c.99C>T
  • NM_001276761.3:c.99C>T
  • NP_000537.3:p.Pro72=
  • NP_000537.3:p.Pro72=
  • NP_001119584.1:p.Pro72=
  • NP_001119585.1:p.Pro72=
  • NP_001119586.1:p.Pro72=
  • NP_001119590.1:p.Pro33=
  • NP_001263624.1:p.Pro33=
  • NP_001263625.1:p.Pro33=
  • NP_001263689.1:p.Pro33=
  • NP_001263690.1:p.Pro33=
  • LRG_321t1:c.216C>T
  • LRG_321:g.16398C>T
  • LRG_321p1:p.Pro72=
  • NC_000017.10:g.7579471G>A
  • NM_000546.4:c.216C>T
  • NM_000546.5:c.216C>T
  • p.P72P
Links:
dbSNP: rs56275308
NCBI 1000 Genomes Browser:
rs56275308
Molecular consequence:
  • NM_000546.6:c.216C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126112.3:c.216C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126113.3:c.216C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126114.3:c.216C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126118.2:c.99C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276695.3:c.99C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276696.3:c.99C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276760.3:c.99C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276761.3:c.99C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000697437Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Apr 27, 2017) 		germlineclinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Association of p53 codon 72 polymorphism with risk of hypopharyngeal squamous cell carcinoma in Taiwan.

Twu CW, Jiang RS, Shu CH, Lin JC.

J Formos Med Assoc. 2006 Feb;105(2):99-104.

PubMed [citation]
PMID:
16477330

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697437.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: The TP53 c.216C>T (p.Pro72Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 7/120822 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.000602 (6/9970). This frequency is about 15 times the estimated maximal expected allele frequency of a pathogenic TP53 variant (0.0000398), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024