NM_000548.5:c.2742+4G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_000548.5(TSC2):c.2742+4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

TSC2
NM_000548.5 splice_region, intron

Scores

Splicing: ADA: 0.00003587

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.123

Publications

1 publications found

Variant links:

Genes affected

TSC2 (HGNC:12363): (TSC complex subunit 2) This gene is a tumor suppressor gene that encodes the growth inhibitory protein tuberin. Tuberin interacts with hamartin to form the TSC protein complex which functions in the control of cell growth. This TSC protein complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]

TSC2 Gene-Disease associations (from GenCC):

tuberous sclerosis
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
tuberous sclerosis 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Ambry Genetics
lymphangioleiomyomatosis
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
tuberous sclerosis complex
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TSC2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 16-2076174-G-A is Benign according to our data. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076174-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 141356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAdExome4 at 19 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSC2	NM_000548.5 link	c.2742+4G>A		splice_region_variant, intron_variant	Intron 24 of 41	ENST00000219476.9	NP_000539.2	P49815-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSC2	ENST00000219476.9 link	c.2742+4G>A		splice_region_variant, intron_variant	Intron 24 of 41	5	NM_000548.5	ENSP00000219476.3		P49815-1

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000240

AC:

AN:

250256

AF XY:

0.0000295

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000532

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000130

AC:

AN:

1461290

Hom.:

Cov.:

AF XY:

0.00000963

AC XY:

AN XY:

726962

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39700

South Asian (SAS)

AF:

0.0000116

AC:

AN:

86248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52872

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.0000135

AC:

AN:

1111996

Other (OTH)

AF:

0.0000166

AC:

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152166

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41438

American (AMR)

AF:

0.00

AC:

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000441

AC:

AN:

68028

Other (OTH)

AF:

0.00

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000267

Hom.:

Bravo

AF:

0.0000151

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Tuberous sclerosis 2

Benign:3

Nov 07, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

May 21, 2025

Myriad Genetics, Inc.

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -

Oct 16, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Feb 05, 2018

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Hereditary cancer-predisposing syndrome

Benign:1

Sep 28, 2015

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

(source)

DANN

Benign

0.47

PhyloP100

-0.12

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000036

dbscSNV1_RF

Benign

0.064

SpliceAI score (max)

0.18

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over