NM_000548.5(TSC2):c.134_138+1delinsC AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 22, 2016
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:: RCV000414690.1

Allele description [Variation Report for NM_000548.5(TSC2):c.134_138+1delinsC]

NM_000548.5(TSC2):c.134_138+1delinsC

Gene:

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

Variant type:

Indel

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.134_138+1delinsC

HGVS:

NC_000016.10:g.2048749_2048754delinsC
NG_005895.1:g.4444_4449delinsC
NG_008412.1:g.4113_4118delinsG
NM_000548.5:c.134_138+1delinsCMANE SELECT
NM_001077183.3:c.134_138+1delinsC
NM_001114382.3:c.134_138+1delinsC
NM_001318827.2:c.134_138+1delinsC
NM_001318829.2:c.-10+684_-10+689delinsC
NM_001318831.2:c.-93_-89+1delinsC
NM_001318832.2:c.167_171+1delinsC
NM_001363528.2:c.134_138+1delinsC
NM_001370404.1:c.134_138+1delinsC
NM_001370405.1:c.134_138+1delinsC
NM_021055.3:c.134_138+1delinsC
LRG_487t1:c.134_138+1delTGAGAGinsC
LRG_1366:g.4113_4118delinsG
LRG_487:g.4444_4449delinsC
NC_000016.9:g.2098750_2098755delinsC
NM_000548.3:c.134_138+1delTGAGAGinsC

Links:

dbSNP: rs1057518535

NCBI 1000 Genomes Browser:

rs1057518535

Molecular consequence:

NM_001318829.2:c.-10+684_-10+689delinsC - intron variant - [Sequence Ontology: SO:0001627]
NM_000548.5:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001077183.3:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001114382.3:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001318827.2:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001318831.2:c.-93_-89+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001318832.2:c.167_171+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001363528.2:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001370404.1:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001370405.1:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]
NM_021055.3:c.134_138+1delinsC - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000492278	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Nov 22, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000492278

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Nov 22, 2016)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000492278.2

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

Description

The c.134_138+1delTGAGAGinsC splice site variant in the TSC2 gene destroys the canonical splice donor site in intron 2. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.

#	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 5, 2022

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