rs2234235

Positions:

• chr5-9629183-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_019599.3(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 NM_019599.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R1	NM_019599.3	c.850T>C	p.Leu284Leu	synonymous_variant	1/1	ENST00000382492.4	NP_062545.1
TAS2R1	NM_001386348.1	c.730T>C	p.Leu244Leu	synonymous_variant	10/10		NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R1	ENST00000382492.4	c.850T>C	p.Leu284Leu	synonymous_variant	1/1	6	NM_019599.3	ENSP00000371932.2
ENSG00000248525	ENST00000504182.2	n.36-5581T>C		intron_variant		5

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

GnomAD3 exomes AF: 0.0312 AC: 7193 AN: 230806 Hom.: 132 AF XY: 0.0326 AC XY: 4082 AN XY: 125192

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 SAS exome AF: 0.0393

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

Gnomad4 AFR exome AF: 0.0198

Gnomad4 AMR exome AF: 0.0197

Gnomad4 ASJ exome AF: 0.0513

Gnomad4 EAS exome AF: 0.000152

Gnomad4 SAS exome AF: 0.0378

Gnomad4 FIN exome AF: 0.0295

Gnomad4 NFE exome AF: 0.0344

Gnomad4 OTH exome AF: 0.0341

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

Gnomad4 AFR AF: 0.0208

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0364

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0341 Hom.: 126

Bravo AF: 0.0276

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	11
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs2234235; hg19: chr5-9629295;