NM_000546.6(TP53):c.354A>T (p.Thr118=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Jun 18, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000163547.8

Allele description [Variation Report for NM_000546.6(TP53):c.354A>T (p.Thr118=)]

NM_000546.6(TP53):c.354A>T (p.Thr118=)

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.354A>T (p.Thr118=)

HGVS:

NC_000017.11:g.7676015T>A
NG_017013.2:g.16536A>T
NM_000546.6:c.354A>TMANE SELECT
NM_001126112.3:c.354A>T
NM_001126113.3:c.354A>T
NM_001126114.3:c.354A>T
NM_001126118.2:c.237A>T
NM_001276695.3:c.237A>T
NM_001276696.3:c.237A>T
NM_001276760.3:c.237A>T
NM_001276761.3:c.237A>T
NP_000537.3:p.Thr118=
NP_000537.3:p.Thr118=
NP_001119584.1:p.Thr118=
NP_001119585.1:p.Thr118=
NP_001119586.1:p.Thr118=
NP_001119590.1:p.Thr79=
NP_001263624.1:p.Thr79=
NP_001263625.1:p.Thr79=
NP_001263689.1:p.Thr79=
NP_001263690.1:p.Thr79=
LRG_321t1:c.354A>T
LRG_321:g.16536A>T
LRG_321p1:p.Thr118=
NC_000017.10:g.7579333T>A
NM_000546.4:c.354A>T
NM_000546.5:c.354A>T
p.T118T
p.Thr118Thr

Links:

dbSNP: rs751978853

NCBI 1000 Genomes Browser:

rs751978853

Molecular consequence:

NM_000546.6:c.354A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.354A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.354A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.354A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.237A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276695.3:c.237A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276696.3:c.237A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.237A>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.237A>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000214105	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Likely benign (Jun 1, 2015)	germline	clinical testing	Citation Link,
SCV000911992	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 25, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002530449	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Jan 25, 2022)	germline	curation	Citation Link,
SCV002582253	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jun 18, 2022)	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	1	not provided	clinical testing, curation
not provided	germline	no	not provided	not provided	not provided	not provided	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 Ambry Genetics, SCV000214105.6

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

Description

This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

From Color Diagnostics, LLC DBA Color Health, SCV000911992.1

#	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

From Sema4, Sema4, SCV002530449.1

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

#	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

From Genome-Nilou Lab, SCV002582253.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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