NM_000546.6(TP53):c.6G>A (p.Glu2=) AND Li-Fraumeni syndrome 1

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 11, 2023
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:: RCV000411973.12

Allele description [Variation Report for NM_000546.6(TP53):c.6G>A (p.Glu2=)]

NM_000546.6(TP53):c.6G>A (p.Glu2=)

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.6G>A (p.Glu2=)

HGVS:

NC_000017.11:g.7676589C>T
NG_017013.2:g.15962G>A
NM_000546.6:c.6G>AMANE SELECT
NM_001126112.3:c.6G>A
NM_001126113.3:c.6G>A
NM_001126114.3:c.6G>A
NM_001126118.2:c.-229G>A
NM_001276695.3:c.-112G>A
NM_001276696.3:c.-112G>A
NM_001276760.3:c.-112G>A
NM_001276761.3:c.-112G>A
NP_000537.3:p.Glu2=
NP_000537.3:p.Glu2=
NP_001119584.1:p.Glu2=
NP_001119585.1:p.Glu2=
NP_001119586.1:p.Glu2=
LRG_321t1:c.6G>A
LRG_321:g.15962G>A
LRG_321p1:p.Glu2=
NC_000017.10:g.7579907C>T
NM_000546.4:c.6G>A
NM_000546.5:c.6G>A
p.E2E
p.Glu2Glu

Links:

dbSNP: rs143458271

NCBI 1000 Genomes Browser:

rs143458271

Molecular consequence:

NM_001126118.2:c.-229G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276695.3:c.-112G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276696.3:c.-112G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276760.3:c.-112G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276761.3:c.-112G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.6G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.6G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.6G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.6G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Li-Fraumeni syndrome 1 (LFS)
Identifiers:: Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

Recent activity

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Amblystigma cionophorum (0)
Nucleotide
Avena altissima (0)
Nucleotide
Salmonella enterica subsp. enterica serovar Typhi genome assembly 10060_6#44, sc...
Salmonella enterica subsp. enterica serovar Typhi genome assembly 10060_6#44, scaffold ERS223550SCcontig000024, whole genome shotgun sequence
gi|874931520|emb|CIOY01000024.1|

Nucleotide
Salmonella enterica subsp. enterica serovar Typhi genome assembly 10060_6#20, sc...
Salmonella enterica subsp. enterica serovar Typhi genome assembly 10060_6#20, scaffold ERS223526SCcontig000014, whole genome shotgun sequence
gi|874970910|emb|CIOK01000014.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000488031	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Dec 14, 2015)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID] Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV002582989	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]
SCV004017839	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Apr 11, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000488031

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Likely benign
(Dec 14, 2015)

unknown

clinical testing

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

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV002582989

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]

SCV004017839

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Benign
(Apr 11, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification and characterization of the unique guanine nucleotide exchange factor, SmgGDS, in vascular smooth muscle cells.

Thill R, Campbell WB, Williams CL.

J Cell Biochem. 2008 Aug 1;104(5):1760-70. doi: 10.1002/jcb.21740.

PubMed [citation]

PMID:: 18348285

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 Counsyl, SCV000488031.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002582989.1

#	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

From Myriad Genetics, Inc., SCV004017839.1

#	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 considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.

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

Last Updated: Nov 3, 2024

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