rs2234233

Variant names:

• chr5-9629417-G-A
• rs2234233
• NM_019599.3:c.616C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-9629417-G-A
• chr5-9629417-G-C
• chr5-9629417-G-T

Variant summary

Our verdict is Benign. The variant received -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. 15/21 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 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
• Publications: 34 publications found

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]

ENSG00000248525 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TAS2R1	NM_019599.3	c.616C>T	p.Arg206Trp	missense_variant	Exon 1 of 1	ENST00000382492.4	NP_062545.1
TAS2R1	NM_001386348.1	c.496C>T	p.Arg166Trp	missense_variant	Exon 10 of 10		NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R1	ENST00000382492.4	c.616C>T	p.Arg206Trp	missense_variant	Exon 1 of 1	6	NM_019599.3	ENSP00000371932.2
ENSG00000248525	ENST00000504182.2	n.36-5815C>T		intron_variant	Intron 1 of 2	5
TAS2R1	ENST00000514078.1	c.*29C>T		downstream_gene_variant		3		ENSP00000476190.1

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

GnomAD2 exomes AF: 0.150 AC: 37655 AN: 250762 AF XY: 0.155

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 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

African (AFR) AF: 0.0443 AC: 1484 AN: 33478

American (AMR) AF: 0.116 AC: 5180 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 4612 AN: 26130

East Asian (EAS) AF: 0.131 AC: 5218 AN: 39696

South Asian (SAS) AF: 0.179 AC: 15465 AN: 86252

European-Finnish (FIN) AF: 0.162 AC: 8636 AN: 53410

Middle Eastern (MID) AF: 0.137 AC: 789 AN: 5766

European-Non Finnish (NFE) AF: 0.169 AC: 188302 AN: 1112002

Other (OTH) AF: 0.158 AC: 9546 AN: 60396

GnomAD4 genome AF: 0.133 AC: 20240 AN: 152100 Hom.: 1557 Cov.: 32 AF XY: 0.132 AC XY: 9848 AN XY: 74342

African (AFR) AF: 0.0519 AC: 2153 AN: 41504

American (AMR) AF: 0.133 AC: 2038 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3472

East Asian (EAS) AF: 0.124 AC: 639 AN: 5158

South Asian (SAS) AF: 0.182 AC: 878 AN: 4812

European-Finnish (FIN) AF: 0.155 AC: 1634 AN: 10572

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11804 AN: 67980

Other (OTH) AF: 0.131 AC: 277 AN: 2112

Alfa AF: 0.157 Hom.: 5966

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
PhyloP100		-0.13
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
Mutation Taster		=98/2	polymorphism (auto)

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