NM_000548.5(TSC2):c.1869C>T (p.Ala623=) AND Tuberous sclerosis syndrome

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Feb 5, 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:: RCV000381430.14

Allele description [Variation Report for NM_000548.5(TSC2):c.1869C>T (p.Ala623=)]

NM_000548.5(TSC2):c.1869C>T (p.Ala623=)

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.1869C>T (p.Ala623=)

Other names:

p.A623A:GCC>GCT; p.Ala623Ala

HGVS:

NC_000016.10:g.2071539C>T
NG_005895.1:g.27234C>T
NM_000548.5:c.1869C>TMANE SELECT
NM_001077183.3:c.1869C>T
NM_001114382.3:c.1869C>T
NM_001318827.2:c.1758C>T
NM_001318829.2:c.1722C>T
NM_001318831.2:c.1269C>T
NM_001318832.2:c.1902C>T
NM_001363528.2:c.1869C>T
NM_001370404.1:c.1869C>T
NM_001370405.1:c.1869C>T
NM_021055.3:c.1869C>T
NP_000539.2:p.Ala623=
NP_001070651.1:p.Ala623=
NP_001107854.1:p.Ala623=
NP_001305756.1:p.Ala586=
NP_001305758.1:p.Ala574=
NP_001305760.1:p.Ala423=
NP_001305761.1:p.Ala634=
NP_001350457.1:p.Ala623=
NP_001357333.1:p.Ala623=
NP_001357334.1:p.Ala623=
NP_066399.2:p.Ala623=
LRG_487t1:c.1869C>T
LRG_487:g.27234C>T
NC_000016.9:g.2121540C>T
NM_000548.3:c.1869C>T
NM_000548.4:c.1869C>T
p.A623A

Links:

dbSNP: rs111244727

NCBI 1000 Genomes Browser:

rs111244727

Molecular consequence:

NM_000548.5:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.1758C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.1269C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.1902C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.1869C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

101

Condition(s)

Name:: Tuberous sclerosis syndrome (TSC)
Synonyms:: Tuberous sclerosis
Identifiers:: MONDO: MONDO:0001734; MedGen: C0041341; OMIM: PS191100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000395594	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Likely benign (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV004814937	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Feb 5, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000395594

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification 20161018)

Likely benign
(Jun 14, 2016)

germline

clinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV004814937

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Feb 5, 2024)

germline

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	unknown	101	not provided	not provided	108544	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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000395594.2

#	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

From All of Us Research Program, National Institutes of Health, SCV004814937.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	101	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	unknown	108544	not provided	not provided		101	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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