rs2234233

chr5-9629417-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R206Q) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.13 (1557 hom., cov: 32)
  • Exomes 𝑓: 0.16 (20207 hom.)
• Consequence: TAS2R1 NM_019599.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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]

(HGNC:):

ACMG classification

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	UniProt
TAS2R1	NM_019599.3	c.616C>T	p.Arg206Trp	missense_variant	1/1	ENST00000382492.4
TAS2R1	NM_001386348.1	c.496C>T	p.Arg166Trp	missense_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS2R1	ENST00000382492.4	c.616C>T	p.Arg206Trp	missense_variant	1/1		NM_019599.3	P1
	ENST00000504182.2	n.36-5815C>T		intron_variant, non_coding_transcript_variant		5
TAS2R1	ENST00000514078.1			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20234 AN: 151984 Hom.: 1558 Cov.: 32

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

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.: 33 AF XY: 0.164 AC XY: 119605 AN XY: 727220

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.: 32 AF XY: 0.132 AC XY: 9848 AN XY: 74342

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	T
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.9
Dann	Benign	0.74
DEOGEN2	Benign	0.069	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.51	T
MetaRNN	Benign	0.0030	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.36	N
MutationTaster	Benign	1.0	P
PrimateAI	Benign	0.16	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.024
Sift	Benign	0.10	T
Sift4G	Uncertain	0.054	T
Polyphen		0.0020	B
Vest4		0.070
MPC		0.021
ClinPred		0.022	T
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

Other links and lift over

dbSNP: rs2234233; hg19: chr5-9629529; COSMIC: COSV66778295; COSMIC: COSV66778295;