rs1555495692

Variant names:

• chr16-2050408-C-A
• rs1555495692
• NM_000548.5:c.147C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-2050408-C-A
• chr16-2050408-C-G
• chr16-2050408-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM1 PM2

The NM_000548.5(TSC2):​c.147C>A​(p.Ser49Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S49N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: TSC2 NM_000548.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 0 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: Uncertain_significance. The variant received 4 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 8 benign, 13 uncertain in NM_000548.5
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSC2	NM_000548.5	c.147C>A	p.Ser49Arg	missense_variant	Exon 3 of 42	ENST00000219476.9	NP_000539.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSC2	ENST00000219476.9	c.147C>A	p.Ser49Arg	missense_variant	Exon 3 of 42	5	NM_000548.5	ENSP00000219476.3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.68
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.060
CADD	Benign	17
DANN	Uncertain	0.99
DEOGEN2	Benign	0.41	T;.;.;.;.;.;.;.;.;.;.;.;T;.;T
Eigen	Benign	-0.50
Eigen_PC	Benign	-0.62
FATHMM_MKL	Benign	0.12	N
LIST_S2	Uncertain	0.97	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Uncertain	0.47	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.51	T
MutationAssessor	Benign	1.2	L;.;.;L;L;.;.;L;L;.;.;L;.;.;.
PhyloP100		-0.23
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.6	N;.;.;.;N;.;.;N;N;.;.;.;.;.;N
REVEL	Uncertain	0.42
Sift	Uncertain	0.012	D;.;.;.;D;.;.;D;D;.;.;.;.;.;D
Sift4G	Benign	0.063	T;.;.;.;T;.;.;T;T;.;.;.;.;.;T
Polyphen		1.0	D;.;.;.;D;.;.;P;P;.;.;.;.;.;.
Vest4		0.70
MutPred		0.43		Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);Gain of MoRF binding (P = 0.0198);.;
MVP		0.82
ClinPred		0.94	D
GERP RS		1.2
Varity_R		0.093
gMVP		0.49
Mutation Taster		=78/22	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1555495692; hg19: chr16-2100409;