NM_000548.5:c.2784delC

Variant names:

• chr16-2076527-AC-A
• rs34245038
• NM_000548.5:c.2784delC

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000548.5(TSC2):​c.2784delC​(p.Glu929ArgfsTer19) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P928P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TSC2 NM_000548.5 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2 O:1
• Conservation: PhyloP100: 5.68
• Publications: 2 publications found

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

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 16-2076527-AC-A is Pathogenic according to our data. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2076527-AC-A is described in CliVar as Pathogenic. Clinvar id is 49232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSC2	NM_000548.5	c.2784delC	p.Glu929ArgfsTer19	frameshift_variant	Exon 25 of 42	ENST00000219476.9	NP_000539.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSC2	ENST00000219476.9	c.2784delC	p.Glu929ArgfsTer19	frameshift_variant	Exon 25 of 42	5	NM_000548.5	ENSP00000219476.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461314 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 726940

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52880

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111990

Other (OTH) AF: 0.00 AC: 0 AN: 60382

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Tuberous sclerosis 2 Pathogenic:1

Apr 24, 2024

Molecular Pathology, Peter Maccallum Cancer Centre

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Feb 12, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 9829910) -

Tuberous sclerosis syndrome Other:1

-

Tuberous sclerosis database (TSC2)

Significance: not provided

Review Status: no classification provided

Collection Method: curation

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.7
Mutation Taster		=0/200	disease causing (fs/PTC)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs34245038; hg19: chr16-2126528; COSMIC: COSV54783595; COSMIC: COSV54783595;