NM_000546.6(TP53):c.993+227A>C AND Li-Fraumeni syndrome 1

Germline classification:: Likely benign (2 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:: RCV000412277.5

Allele description [Variation Report for NM_000546.6(TP53):c.993+227A>C]

NM_000546.6(TP53):c.993+227A>C

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.993+227A>C

Other names:

*210S; *342S; *303S; *183S

HGVS:

NC_000017.11:g.7673308T>G
NG_017013.2:g.19243A>C
NM_000546.6:c.993+227A>CMANE SELECT
NM_001126112.3:c.993+227A>C
NM_001126113.3:c.994-42A>C
NM_001126114.3:c.1025A>C
NM_001126115.2:c.597+227A>C
NM_001126116.2:c.629A>C
NM_001126117.2:c.598-42A>C
NM_001126118.2:c.876+227A>C
NM_001276695.3:c.877-42A>C
NM_001276696.3:c.908A>C
NM_001276697.3:c.516+227A>C
NM_001276698.3:c.548A>C
NM_001276699.3:c.517-42A>C
NM_001276760.3:c.876+227A>C
NM_001276761.3:c.876+227A>C
NP_001119586.1:p.Ter342Ser
NP_001119588.1:p.Ter210Ser
NP_001263625.1:p.Ter303Ser
NP_001263627.1:p.Ter183Ser
LRG_321t1:c.993+227A>C
LRG_321:g.19243A>C
NC_000017.10:g.7576626T>G
NM_000546.5:c.993+227A>C

Links:

dbSNP: rs764562217

NCBI 1000 Genomes Browser:

rs764562217

Molecular consequence:

NM_000546.6:c.993+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.993+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.994-42A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126115.2:c.597+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126117.2:c.598-42A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126118.2:c.876+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.877-42A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276697.3:c.516+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276699.3:c.517-42A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.876+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.876+227A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.1025A>C - stop lost - [Sequence Ontology: SO:0001578]
NM_001126116.2:c.629A>C - stop lost - [Sequence Ontology: SO:0001578]
NM_001276696.3:c.908A>C - stop lost - [Sequence Ontology: SO:0001578]
NM_001276698.3:c.548A>C - stop lost - [Sequence Ontology: SO:0001578]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000489477	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Oct 13, 2016)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV002582790	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]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000489477

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Likely benign
(Oct 13, 2016)

unknown

clinical testing

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV002582790

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	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

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, SCV000489477.2

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

#	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, SCV002582790.1

#	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: Dec 24, 2023

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