NM_000548.5(TSC2):c.1656A>G (p.Ala552=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Sep 7, 2021
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:: RCV001012581.10

Allele description [Variation Report for NM_000548.5(TSC2):c.1656A>G (p.Ala552=)]

NM_000548.5(TSC2):c.1656A>G (p.Ala552=)

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.1656A>G (p.Ala552=)

HGVS:

NC_000016.10:g.2065575A>G
NG_005895.1:g.21270A>G
NM_000548.5:c.1656A>GMANE SELECT
NM_001077183.3:c.1656A>G
NM_001114382.3:c.1656A>G
NM_001318827.2:c.1545A>G
NM_001318829.2:c.1509A>G
NM_001318831.2:c.1056A>G
NM_001318832.2:c.1689A>G
NM_001363528.2:c.1656A>G
NM_001370404.1:c.1656A>G
NM_001370405.1:c.1656A>G
NM_021055.3:c.1656A>G
NP_000539.2:p.Ala552=
NP_001070651.1:p.Ala552=
NP_001107854.1:p.Ala552=
NP_001305756.1:p.Ala515=
NP_001305758.1:p.Ala503=
NP_001305760.1:p.Ala352=
NP_001305761.1:p.Ala563=
NP_001350457.1:p.Ala552=
NP_001357333.1:p.Ala552=
NP_001357334.1:p.Ala552=
NP_066399.2:p.Ala552=
LRG_487t1:c.1656A>G
LRG_487:g.21270A>G
NC_000016.9:g.2115576A>G
NM_000548.3:c.1656A>G
p.(=)

Links:

Tuberous sclerosis database (TSC2): TSC2_02350; dbSNP: rs373515515

NCBI 1000 Genomes Browser:

rs373515515

Molecular consequence:

NM_000548.5:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.1545A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.1509A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.1056A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.1689A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.1656A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001173050	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Likely benign (Nov 5, 2015)	germline	clinical testing	Citation Link,
SCV002530981	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Sep 7, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001173050

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Likely benign
(Nov 5, 2015)

germline

clinical testing

Citation Link,

SCV002530981

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Sep 7, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	1	not provided	clinical testing, curation

Details of each submission

From Ambry Genetics, SCV001173050.3

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

Description

This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided

From Sema4, Sema4, SCV002530981.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	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: Apr 6, 2024

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