NM_000548.5(TSC2):c.1839+4T>C AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 9, 2023
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:: RCV003302846.2

Allele description [Variation Report for NM_000548.5(TSC2):c.1839+4T>C]

NM_000548.5(TSC2):c.1839+4T>C

Gene:

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.1839+4T>C

HGVS:

NC_000016.10:g.2070582T>C
NG_005895.1:g.26277T>C
NM_000548.5:c.1839+4T>CMANE SELECT
NM_001077183.3:c.1839+4T>C
NM_001114382.3:c.1839+4T>C
NM_001318827.2:c.1728+4T>C
NM_001318829.2:c.1692+4T>C
NM_001318831.2:c.1239+4T>C
NM_001318832.2:c.1872+4T>C
NM_001363528.2:c.1839+4T>C
NM_001370404.1:c.1839+4T>C
NM_001370405.1:c.1839+4T>C
NM_021055.3:c.1839+4T>C
LRG_487t1:c.1839+4T>C
LRG_487:g.26277T>C
NC_000016.9:g.2120583T>C
NM_000548.3:c.1839+4T>C

Links:

dbSNP: rs1246472342

NCBI 1000 Genomes Browser:

rs1246472342

Molecular consequence:

NM_000548.5:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001077183.3:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001114382.3:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318827.2:c.1728+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318829.2:c.1692+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318831.2:c.1239+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001318832.2:c.1872+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001363528.2:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001370404.1:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001370405.1:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_021055.3:c.1839+4T>C - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

Clear Turn Off Turn On

Homo sapiens isolate CHM13 chromosome 1, alternate assembly T2T-CHM13v2.0
Homo sapiens isolate CHM13 chromosome 1, alternate assembly T2T-CHM13v2.0
gi|2194974903|gnl|ASM:GCF_009914825 f|NC_060925.1||gpp|GPC_000012740.1||gnl|NCBI_GENOMES|119561

Nucleotide

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
SCV003988642	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 9, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003988642

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 9, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003988642.2

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

Description

The c.1839+4T>C intronic variant results from a T to C substitution 4 nucleotides after coding exon 16 in the TSC2 gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine