Variant 6-132617703-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001033080.1(TAAR2):c.503G>A(p.Trp168Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0269 in 1,613,828 control chromosomes in the GnomAD database, including 1,203 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.026 ( 127 hom., cov: 32)

Exomes 𝑓: 0.027 ( 1076 hom. )

Consequence

TAAR2
NM_001033080.1 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.06

Variant links:

Genes affected

TAAR2 (HGNC:4514): (trace amine associated receptor 2) Predicted to enable trace-amine receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TAAR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAAR2	NM_001033080.1 linkuse as main transcript	c.503G>A	p.Trp168Ter	stop_gained	2/2	ENST00000367931.1
TAAR2	NM_014626.3 linkuse as main transcript	c.368G>A	p.Trp123Ter	stop_gained	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAAR2	ENST00000367931.1 linkuse as main transcript	c.503G>A	p.Trp168Ter	stop_gained	2/2	1	NM_001033080.1	A2	Q9P1P5-1
TAAR2	ENST00000275191.2 linkuse as main transcript	c.368G>A	p.Trp123Ter	stop_gained	1/1			P4	Q9P1P5-2

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3990

AN:

152058

Hom.:

126

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0128

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0154

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0676

Gnomad FIN

AF:

0.0140

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0248

Gnomad OTH

AF:

0.0220

GnomAD3 exomes

AF:

0.0364

AC:

9079

AN:

249504

Hom.:

506

AF XY:

0.0378

AC XY:

5107

AN XY:

134982

show subpopulations

Gnomad AFR exome

AF:

0.0124

Gnomad AMR exome

AF:

0.00808

Gnomad ASJ exome

AF:

0.0147

Gnomad EAS exome

AF:

0.197

Gnomad SAS exome

AF:

0.0571

Gnomad FIN exome

AF:

0.0158

Gnomad NFE exome

AF:

0.0230

Gnomad OTH exome

AF:

0.0297

GnomAD4 exome

AF:

0.0270

AC:

39473

AN:

1461652

Hom.:

1076

Cov.:

AF XY:

0.0282

AC XY:

20478

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.0135

Gnomad4 AMR exome

AF:

0.00816

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.140

Gnomad4 SAS exome

AF:

0.0583

Gnomad4 FIN exome

AF:

0.0149

Gnomad4 NFE exome

AF:

0.0220

Gnomad4 OTH exome

AF:

0.0357

GnomAD4 genome

AF:

0.0262

AC:

3990

AN:

152176

Hom.:

127

Cov.:

AF XY:

0.0267

AC XY:

1985

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0127

Gnomad4 AMR

AF:

0.0154

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.186

Gnomad4 SAS

AF:

0.0679

Gnomad4 FIN

AF:

0.0140

Gnomad4 NFE

AF:

0.0248

Gnomad4 OTH

AF:

0.0251

Alfa

AF:

0.0258

Hom.:

211

Bravo

AF:

0.0247

TwinsUK

AF:

0.0248

AC:

ALSPAC

AF:

0.0179

AC:

ESP6500AA

AF:

0.0141

AC:

ESP6500EA

AF:

0.0219

AC:

188

ExAC

AF:

0.0362

AC:

4398

Asia WGS

AF:

0.119

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.20

BayesDel_noAF

Pathogenic

0.66

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.77

Eigen_PC

Uncertain

0.62

FATHMM_MKL

Uncertain

0.97

MutationTaster

Benign

1.4e-22

P;P;P

Vest4

0.24

GERP RS

6.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over