NM_000548.5(TSC2):c.2979G>A (p.Thr993=) AND not specified

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Jul 11, 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:: RCV000125668.15

Allele description [Variation Report for NM_000548.5(TSC2):c.2979G>A (p.Thr993=)]

NM_000548.5(TSC2):c.2979G>A (p.Thr993=)

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.2979G>A (p.Thr993=)

Other names:

p.T993T:ACG>ACA

HGVS:

NC_000016.10:g.2079044G>A
NG_005895.1:g.34739G>A
NM_000548.5:c.2979G>AMANE SELECT
NM_001077183.3:c.2847G>A
NM_001114382.3:c.2979G>A
NM_001318827.2:c.2739G>A
NM_001318829.2:c.2703G>A
NM_001318831.2:c.2247G>A
NM_001318832.2:c.2880G>A
NM_001363528.2:c.2850G>A
NM_001370404.1:c.2847G>A
NM_001370405.1:c.2850G>A
NM_021055.3:c.2850G>A
NP_000539.2:p.Thr993=
NP_001070651.1:p.Thr949=
NP_001107854.1:p.Thr993=
NP_001305756.1:p.Thr913=
NP_001305758.1:p.Thr901=
NP_001305760.1:p.Thr749=
NP_001305761.1:p.Thr960=
NP_001350457.1:p.Thr950=
NP_001357333.1:p.Thr949=
NP_001357334.1:p.Thr950=
NP_066399.2:p.Thr950=
LRG_487t1:c.2979G>A
LRG_487:g.34739G>A
NC_000016.9:g.2129045G>A
NM_000548.3:c.2979G>A
NM_000548.4:c.2979G>A
p.T993T
p.(=)

Links:

Tuberous sclerosis database (TSC2): TSC2_00491; dbSNP: rs45517277

NCBI 1000 Genomes Browser:

rs45517277

Molecular consequence:

NM_000548.5:c.2979G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.2847G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.2979G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.2739G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.2703G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.2247G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.2880G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.2850G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.2847G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.2850G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.2850G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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
SCV000169130	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Oct 11, 2013)	germline	clinical testing	Citation Link,
SCV000855618	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Jul 13, 2017)	germline	clinical testing	Citation Link,
SCV001972190	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Benign	germline	clinical testing
SCV002774073	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Aug 3, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005202655	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jul 11, 2024)	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
not provided	germline	unknown	1	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

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 GeneDx, SCV000169130.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Eurofins Ntd Llc (ga), SCV000855618.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001972190.1

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002774073.1

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005202655.1

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

Last Updated: Oct 8, 2024

ClinVar

Relating variation to medicine