rs2234235

Variant names:

• chr5-9629183-A-G
• rs2234235
• NM_019599.3:c.850T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The ENST00000382492.4(TAS2R1):​c.850T>C​(p.Leu284Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,590,698 control chromosomes in the GnomAD database, including 944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.028 (74 hom., cov: 32)
  • Exomes 𝑓: 0.033 (870 hom.)
• Consequence: TAS2R1 ENST00000382492.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 8 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP7: Synonymous conserved (PhyloP=0.147 with no splicing effect.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000382492.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R1	NM_019599.3	MANE Select	c.850T>C	p.Leu284Leu	synonymous	Exon 1 of 1	NP_062545.1
	TAS2R1	NM_001386348.1		c.730T>C	p.Leu244Leu	synonymous	Exon 10 of 10	NP_001373277.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R1	ENST00000382492.4	TSL:6 MANE Select	c.850T>C	p.Leu284Leu	synonymous	Exon 1 of 1	ENSP00000371932.2
	ENSG00000248525	ENST00000504182.2	TSL:5	n.36-5581T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0282 AC: 4288 AN: 152170 Hom.: 74 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0311

GnomAD2 exomes AF: 0.0312 AC: 7193 AN: 230806 AF XY: 0.0326

Gnomad AFR exome AF: 0.0212

Gnomad AMR exome AF: 0.0204

Gnomad ASJ exome AF: 0.0570

Gnomad EAS exome AF: 0.000175

Gnomad FIN exome AF: 0.0279

Gnomad NFE exome AF: 0.0368

Gnomad OTH exome AF: 0.0348

GnomAD4 exome AF: 0.0332 AC: 47694 AN: 1438410 Hom.: 870 Cov.: 30 AF XY: 0.0335 AC XY: 23932 AN XY: 714904

African (AFR) AF: 0.0198 AC: 630 AN: 31854

American (AMR) AF: 0.0197 AC: 750 AN: 38036

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 1261 AN: 24578

East Asian (EAS) AF: 0.000152 AC: 6 AN: 39506

South Asian (SAS) AF: 0.0378 AC: 3147 AN: 83298

European-Finnish (FIN) AF: 0.0295 AC: 1558 AN: 52840

Middle Eastern (MID) AF: 0.0637 AC: 357 AN: 5606

European-Non Finnish (NFE) AF: 0.0344 AC: 37966 AN: 1103536

Other (OTH) AF: 0.0341 AC: 2019 AN: 59156

GnomAD4 genome AF: 0.0282 AC: 4294 AN: 152288 Hom.: 74 Cov.: 32 AF XY: 0.0282 AC XY: 2098 AN XY: 74478

African (AFR) AF: 0.0208 AC: 863 AN: 41550

American (AMR) AF: 0.0235 AC: 359 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0364 AC: 176 AN: 4830

European-Finnish (FIN) AF: 0.0267 AC: 283 AN: 10618

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0340 AC: 2310 AN: 68028

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0329 Hom.: 246

Bravo AF: 0.0276

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2234235; hg19: chr5-9629295;