NM_000546.6(TP53):c.246G>A (p.Pro82=) AND Li-Fraumeni syndrome 1

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jul 7, 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:: RCV002288726.3

Allele description [Variation Report for NM_000546.6(TP53):c.246G>A (p.Pro82=)]

NM_000546.6(TP53):c.246G>A (p.Pro82=)

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.246G>A (p.Pro82=)

HGVS:

NC_000017.11:g.7676123C>T
NG_017013.2:g.16428G>A
NM_000546.6:c.246G>AMANE SELECT
NM_001126112.3:c.246G>A
NM_001126113.3:c.246G>A
NM_001126114.3:c.246G>A
NM_001126118.2:c.129G>A
NM_001276695.3:c.129G>A
NM_001276696.3:c.129G>A
NM_001276760.3:c.129G>A
NM_001276761.3:c.129G>A
NP_000537.3:p.Pro82=
NP_000537.3:p.Pro82=
NP_001119584.1:p.Pro82=
NP_001119585.1:p.Pro82=
NP_001119586.1:p.Pro82=
NP_001119590.1:p.Pro43=
NP_001263624.1:p.Pro43=
NP_001263625.1:p.Pro43=
NP_001263689.1:p.Pro43=
NP_001263690.1:p.Pro43=
LRG_321t1:c.246G>A
LRG_321:g.16428G>A
LRG_321p1:p.Pro82=
NC_000017.10:g.7579441C>T
NM_000546.4:c.246G>A
NM_000546.5:c.246G>A
p.P82P

Links:

dbSNP: rs372397095

NCBI 1000 Genomes Browser:

rs372397095

Molecular consequence:

NM_000546.6:c.246G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.246G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.246G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.246G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.129G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276695.3:c.129G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276696.3:c.129G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.129G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.129G>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

Clear Turn Off Turn On

small nuclear ribonucleoprotein Sm D2 [Cucumis sativus]
small nuclear ribonucleoprotein Sm D2 [Cucumis sativus]
gi|449457536|ref|XP_004146504.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002582931	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]
SCV004015638	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jul 7, 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

SCV002582931

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]

SCV004015638

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jul 7, 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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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 Genome-Nilou Lab, SCV002582931.1

#	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 KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015638.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

ClinVar

Relating variation to medicine