NM_000548.5(TSC2):c.4617A>G (p.Ser1539=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Mar 16, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV001022787.6

Allele description [Variation Report for NM_000548.5(TSC2):c.4617A>G (p.Ser1539=)]

NM_000548.5(TSC2):c.4617A>G (p.Ser1539=)

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.4617A>G (p.Ser1539=)

HGVS:

NC_000016.10:g.2085277A>G
NG_005895.1:g.40972A>G
NM_000548.5:c.4617A>GMANE SELECT
NM_001077183.3:c.4416A>G
NM_001114382.3:c.4548A>G
NM_001318827.2:c.4308A>G
NM_001318829.2:c.4272A>G
NM_001318831.2:c.3885A>G
NM_001318832.2:c.4449A>G
NM_001363528.2:c.4419A>G
NM_001370404.1:c.4485A>G
NM_001370405.1:c.4488A>G
NM_021055.3:c.4488A>G
NP_000539.2:p.Ser1539=
NP_001070651.1:p.Ser1472=
NP_001107854.1:p.Ser1516=
NP_001305756.1:p.Ser1436=
NP_001305758.1:p.Ser1424=
NP_001305760.1:p.Ser1295=
NP_001305761.1:p.Ser1483=
NP_001350457.1:p.Ser1473=
NP_001357333.1:p.Ser1495=
NP_001357334.1:p.Ser1496=
NP_066399.2:p.Ser1496=
LRG_487t1:c.4617A>G
LRG_487:g.40972A>G
NC_000016.9:g.2135278A>G
NM_000548.3:c.4617A>G

Links:

dbSNP: rs201038907

NCBI 1000 Genomes Browser:

rs201038907

Molecular consequence:

NM_000548.5:c.4617A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.4416A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.4548A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.4308A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.4272A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.3885A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.4449A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.4419A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.4485A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.4488A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.4488A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV001184564	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (May 21, 2015)	germline	clinical testing	Citation Link,
SCV002533957	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Mar 16, 2022)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001184564

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(May 21, 2015)

germline

clinical testing

Citation Link,

SCV002533957

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Mar 16, 2022)

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	not provided	not provided	not provided	not provided	not provided	clinical testing, curation

Details of each submission

From Ambry Genetics, SCV001184564.4

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Sema4, Sema4, SCV002533957.1

#	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: Sep 29, 2024

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