Variant rs2234233 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019599.3(TAS2R1):c.616C>T(p.Arg206Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,613,938 control chromosomes in the GnomAD database, including 21,764 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1557 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20207 hom. )

Consequence

TAS2R1
NM_019599.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132

Variant links:

Genes affected

TAS2R1 (HGNC:14909): (taste 2 receptor member 1) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily and that are specifically expressed by taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is mapped to chromosome 5p15, the location of a genetic locus (PROP) that controls the detection of the bitter compound 6-n-propyl-2-thiouracil. [provided by RefSeq, Jul 2008]

TAS2R1 links:

ENSG00000248525 (HGNC:):

ENSG00000248525 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029955506).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R1	NM_019599.3 link	c.616C>T	p.Arg206Trp	missense_variant	1/1	ENST00000382492.4	NP_062545.1	Q9NYW7Q502V6
TAS2R1	NM_001386348.1 link	c.496C>T	p.Arg166Trp	missense_variant	10/10		NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TAS2R1	ENST00000382492.4 link	c.616C>T	p.Arg206Trp	missense_variant	1/1	6	NM_019599.3	ENSP00000371932.2	Q9NYW7
ENSG00000248525	ENST00000504182.2 link	n.36-5815C>T		intron_variant		5
TAS2R1	ENST00000514078.1 link	c.*29C>T		downstream_gene_variant		3		ENSP00000476190.1	U3KQT0

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20234

AN:

151984

Hom.:

1558

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0519

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.131

GnomAD3 exomes

AF:

0.150

AC:

37655

AN:

250762

Hom.:

2960

AF XY:

0.155

AC XY:

20996

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.0514

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.174

Gnomad EAS exome

AF:

0.121

Gnomad SAS exome

AF:

0.178

Gnomad FIN exome

AF:

0.161

Gnomad NFE exome

AF:

0.167

Gnomad OTH exome

AF:

0.156

GnomAD4 exome

AF:

0.164

AC:

239232

AN:

1461838

Hom.:

20207

Cov.:

AF XY:

0.164

AC XY:

119605

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.0443

Gnomad4 AMR exome

AF:

0.116

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.179

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.169

Gnomad4 OTH exome

AF:

0.158

GnomAD4 genome

AF:

0.133

AC:

20240

AN:

152100

Hom.:

1557

Cov.:

AF XY:

0.132

AC XY:

9848

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.0519

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.170

Gnomad4 EAS

AF:

0.124

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.174

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.163

Hom.:

4335

Bravo

AF:

0.127

TwinsUK

AF:

0.165

AC:

611

ALSPAC

AF:

0.167

AC:

644

ESP6500AA

AF:

0.0490

AC:

216

ESP6500EA

AF:

0.165

AC:

1422

ExAC

AF:

0.150

AC:

18204

Asia WGS

AF:

0.143

AC:

497

AN:

3478

EpiCase

AF:

0.165

EpiControl

AF:

0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.9

DANN

Benign

0.74

DEOGEN2

Benign

0.069

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.020

LIST_S2

Benign

0.51

MetaRNN

Benign

0.0030

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.36

PrimateAI

Benign

0.16

PROVEAN

Benign

-1.2

REVEL

Benign

0.024

Sift

Benign

0.10

Sift4G

Uncertain

0.054

Polyphen

0.0020

Vest4

0.070

MPC

0.021

ClinPred

0.022

GERP RS

-11

Varity_R

0.038

gMVP

0.20

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

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