NM_000548.5(TSC2):c.1839+6G>A AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jul 1, 2024
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:: RCV000513698.21

Allele description [Variation Report for NM_000548.5(TSC2):c.1839+6G>A]

NM_000548.5(TSC2):c.1839+6G>A

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+6G>A

HGVS:

NC_000016.10:g.2070584G>A
NG_005895.1:g.26279G>A
NM_000548.5:c.1839+6G>AMANE SELECT
NM_001077183.3:c.1839+6G>A
NM_001114382.3:c.1839+6G>A
NM_001318827.2:c.1728+6G>A
NM_001318829.2:c.1692+6G>A
NM_001318831.2:c.1239+6G>A
NM_001318832.2:c.1872+6G>A
NM_001363528.2:c.1839+6G>A
NM_001370404.1:c.1839+6G>A
NM_001370405.1:c.1839+6G>A
NM_021055.3:c.1839+6G>A
LRG_487t1:c.1839+6G>A
LRG_487:g.26279G>A
NC_000016.9:g.2120585G>A
NM_000548.3:c.1839+6G>A
NM_000548.4:c.1839+6G>A
p.(=)

Links:

Tuberous sclerosis database (TSC2): TSC2_00425; dbSNP: rs45517204

NCBI 1000 Genomes Browser:

rs45517204

Molecular consequence:

NM_000548.5:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001077183.3:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001114382.3:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001318827.2:c.1728+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001318829.2:c.1692+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001318831.2:c.1239+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001318832.2:c.1872+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001363528.2:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001370404.1:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001370405.1:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_021055.3:c.1839+6G>A - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

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
SCV000610731	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 11, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001921449	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002822236	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV004221407	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Feb 19, 2020)	unknown	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	not provided	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
not provided	germline	yes	5	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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000610731.1

#	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	not provided	not provided	not provided	not provided		not provided	0.001201	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001921449.1

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

From CeGaT Center for Human Genetics Tuebingen, SCV002822236.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	5	not provided	not provided	clinical testing	not provided

Description

TSC2: BP4, BS2

#	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		5	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004221407.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine