NM_000548.5(TSC2):c.3162T>C (p.Gly1054=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Mar 16, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002322535.2

Allele description [Variation Report for NM_000548.5(TSC2):c.3162T>C (p.Gly1054=)]

NM_000548.5(TSC2):c.3162T>C (p.Gly1054=)

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.3162T>C (p.Gly1054=)

HGVS:

NC_000016.10:g.2079306T>C
NG_005895.1:g.35001T>C
NM_000548.5:c.3162T>CMANE SELECT
NM_001077183.3:c.3030T>C
NM_001114382.3:c.3162T>C
NM_001318827.2:c.2922T>C
NM_001318829.2:c.2886T>C
NM_001318831.2:c.2430T>C
NM_001318832.2:c.3063T>C
NM_001363528.2:c.3033T>C
NM_001370404.1:c.3030T>C
NM_001370405.1:c.3033T>C
NM_001406663.1:c.3159T>C
NM_001406664.1:c.3159T>C
NM_001406665.1:c.3030T>C
NM_001406667.1:c.3123T>C
NM_001406668.1:c.3120T>C
NM_001406670.1:c.3051T>C
NM_001406671.1:c.3021T>C
NM_001406673.1:c.3018T>C
NM_001406675.1:c.3015T>C
NM_001406676.1:c.3012T>C
NM_001406677.1:c.2973T>C
NM_001406678.1:c.2919T>C
NM_001406679.1:c.2883T>C
NM_001406680.1:c.2562T>C
NM_001406681.1:c.2571T>C
NM_001406682.1:c.2562T>C
NM_001406683.1:c.2562T>C
NM_001406684.1:c.2559T>C
NM_001406685.1:c.2433T>C
NM_001406686.1:c.2433T>C
NM_001406687.1:c.2430T>C
NM_001406688.1:c.2430T>C
NM_001406689.1:c.1818T>C
NM_001406690.1:c.1689T>C
NM_001406691.1:c.1686T>C
NM_001406692.1:c.1689T>C
NM_001406693.1:c.1689T>C
NM_001406694.1:c.1689T>C
NM_001406695.1:c.1686T>C
NM_001406696.1:c.1686T>C
NM_001406697.1:c.1686T>C
NM_001406698.1:c.1428T>C
NM_021055.3:c.3033T>C
NP_000539.2:p.Gly1054=
NP_000539.2:p.Gly1054=
NP_001070651.1:p.Gly1010=
NP_001107854.1:p.Gly1054=
NP_001305756.1:p.Gly974=
NP_001305758.1:p.Gly962=
NP_001305760.1:p.Gly810=
NP_001305761.1:p.Gly1021=
NP_001350457.1:p.Gly1011=
NP_001357333.1:p.Gly1010=
NP_001357334.1:p.Gly1011=
NP_001393592.1:p.Gly1053=
NP_001393593.1:p.Gly1053=
NP_001393594.1:p.Gly1010=
NP_001393596.1:p.Gly1041=
NP_001393597.1:p.Gly1040=
NP_001393599.1:p.Gly1017=
NP_001393600.1:p.Gly1007=
NP_001393602.1:p.Gly1006=
NP_001393604.1:p.Gly1005=
NP_001393605.1:p.Gly1004=
NP_001393606.1:p.Gly991=
NP_001393607.1:p.Gly973=
NP_001393608.1:p.Gly961=
NP_001393609.1:p.Gly854=
NP_001393610.1:p.Gly857=
NP_001393611.1:p.Gly854=
NP_001393612.1:p.Gly854=
NP_001393613.1:p.Gly853=
NP_001393614.1:p.Gly811=
NP_001393615.1:p.Gly811=
NP_001393616.1:p.Gly810=
NP_001393617.1:p.Gly810=
NP_001393618.1:p.Gly606=
NP_001393619.1:p.Gly563=
NP_001393620.1:p.Gly562=
NP_001393621.1:p.Gly563=
NP_001393622.1:p.Gly563=
NP_001393623.1:p.Gly563=
NP_001393624.1:p.Gly562=
NP_001393625.1:p.Gly562=
NP_001393626.1:p.Gly562=
NP_001393627.1:p.Gly476=
NP_066399.2:p.Gly1011=
LRG_487t1:c.3162T>C
LRG_487:g.35001T>C
LRG_487p1:p.Gly1054=
NC_000016.9:g.2129307T>C
NM_000548.3:c.3162T>C
NR_176225.1:n.3183T>C
NR_176226.1:n.3362T>C
NR_176227.1:n.3359T>C
NR_176228.1:n.3180T>C
NR_176229.1:n.3140T>C

Molecular consequence:

NR_176225.1:n.3183T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176226.1:n.3362T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176227.1:n.3359T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176228.1:n.3180T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176229.1:n.3140T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000548.5:c.3162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001077183.3:c.3030T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001114382.3:c.3162T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318827.2:c.2922T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318829.2:c.2886T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318831.2:c.2430T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001318832.2:c.3063T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363528.2:c.3033T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370404.1:c.3030T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370405.1:c.3033T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406663.1:c.3159T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406664.1:c.3159T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406665.1:c.3030T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406667.1:c.3123T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406668.1:c.3120T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406670.1:c.3051T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406671.1:c.3021T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406673.1:c.3018T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406675.1:c.3015T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406676.1:c.3012T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406677.1:c.2973T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406678.1:c.2919T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406679.1:c.2883T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406680.1:c.2562T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406681.1:c.2571T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406682.1:c.2562T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406683.1:c.2562T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406684.1:c.2559T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406685.1:c.2433T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406686.1:c.2433T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406687.1:c.2430T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406688.1:c.2430T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406689.1:c.1818T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406690.1:c.1689T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406691.1:c.1686T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406692.1:c.1689T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406693.1:c.1689T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406694.1:c.1689T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406695.1:c.1686T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406696.1:c.1686T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406697.1:c.1686T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001406698.1:c.1428T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_021055.3:c.3033T>C - 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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LOC129953310 [Eupeodes corollae]
LOC129953310 [Eupeodes corollae]
Gene ID:129953310

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002610113	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Mar 16, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002610113

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Mar 16, 2020)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002610113.2

#	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

Last Updated: Sep 29, 2024

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