NM_000546.6(TP53):c.672+1G>A AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 2, 2022
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:: RCV000786828.4

Allele description [Variation Report for NM_000546.6(TP53):c.672+1G>A]

NM_000546.6(TP53):c.672+1G>A

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.672+1G>A

HGVS:

NC_000017.11:g.7674858C>T
NG_017013.2:g.17693G>A
NM_000546.6:c.672+1G>AMANE SELECT
NM_001126112.3:c.672+1G>A
NM_001126113.3:c.672+1G>A
NM_001126114.3:c.672+1G>A
NM_001126115.2:c.276+1G>A
NM_001126116.2:c.276+1G>A
NM_001126117.2:c.276+1G>A
NM_001126118.2:c.555+1G>A
NM_001276695.3:c.555+1G>A
NM_001276696.3:c.555+1G>A
NM_001276697.3:c.195+1G>A
NM_001276698.3:c.195+1G>A
NM_001276699.3:c.195+1G>A
NM_001276760.3:c.555+1G>A
NM_001276761.3:c.555+1G>A
NM_001407262.1:c.672+1G>A
NM_001407263.1:c.555+1G>A
NM_001407264.1:c.672+1G>A
NM_001407265.1:c.555+1G>A
NM_001407266.1:c.672+1G>A
NM_001407267.1:c.555+1G>A
NM_001407268.1:c.672+1G>A
NM_001407269.1:c.555+1G>A
NM_001407270.1:c.672+1G>A
NM_001407271.1:c.555+1G>A
LRG_321t1:c.672+1G>A
LRG_321:g.17693G>A
NC_000017.10:g.7578176C>T
NM_000546.4:c.672+1G>A
NM_000546.5:c.672+1G>A

Links:

dbSNP: rs863224499

NCBI 1000 Genomes Browser:

rs863224499

Molecular consequence:

NM_000546.6:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126112.3:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126113.3:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126114.3:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126115.2:c.276+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126116.2:c.276+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126117.2:c.276+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126118.2:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276695.3:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276696.3:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276697.3:c.195+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276698.3:c.195+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276699.3:c.195+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276760.3:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276761.3:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407262.1:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407263.1:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407264.1:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407265.1:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407266.1:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407267.1:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407268.1:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407269.1:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407270.1:c.672+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407271.1:c.555+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Functional consequence:

sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071] - Comment(s)

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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"29706-85-2"[CompleteSynonym] (4)
PubChem Compound
Cited in PMC for PubMed (Select 30607345) (3)
PMC
PREDICTED: Mus musculus predicted gene, 31718 (Gm31718), transcript variant X4, ...
PREDICTED: Mus musculus predicted gene, 31718 (Gm31718), transcript variant X4, ncRNA
gi|1039791634|ref|XR_388221.3|

Nucleotide
Francisella noatunensis strain FSC1157 FSC1157_57_len16156, whole genome shotgun...
Francisella noatunensis strain FSC1157 FSC1157_57_len16156, whole genome shotgun sequence
gi|1956170468|ref|NZ_JACVLD01000005 gnl|WGS:NZ_JACVLD01|FSC1157_57_len16156

Nucleotide
Francisella noatunensis strain FSC1157 FSC1157_89_len8238, whole genome shotgun ...
Francisella noatunensis strain FSC1157 FSC1157_89_len8238, whole genome shotgun sequence
gi|1956170500|ref|NZ_JACVLD01000009 gnl|WGS:NZ_JACVLD01|FSC1157_89_len8238

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000925722	MutSpliceDB: a database of splice sites variants effects on splicing, NIH	no classification provided	not provided	not applicable	in vitro	Citation Link,
SCV002559557	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 2, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000925722

MutSpliceDB: a database of splice sites variants effects on splicing, NIH

no classification provided

not provided

not applicable

in vitro

Citation Link,

SCV002559557

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 2, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	in vitro
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From MutSpliceDB: a database of splice sites variants effects on splicing, NIH, SCV000925722.2

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

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

From GeneDx, SCV002559557.2

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

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate a damaging effect: loss of transcriptional activity, reduced cell cycle check point arrest in comparison to wild type (Piao et al., 2013); Not observed at significant frequency in large population cohorts (gnomAD); Observed in at least one case of pediatric osteosarcoma in an individual with a family history consistent with Li-Fraumeni like syndrome (Sakurai et al., 2013); This variant is associated with the following publications: (PMID: 22495821, 22911296, 23409989, 16494995, 27352257, 25149524, 27614696, 22703554, 30720243)

#	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: Aug 11, 2024

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