rs28470550

chr1-18854588-A-Cchr1-18854588-A-Gchr1-18854588-A-T

Variant summary

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

The NM_152232.6(TAS1R2):c.882T>G(p.Thr294=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,613,732 control chromosomes in the GnomAD database, including 79,226 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 0.29 (6595 hom., cov: 33)
  • Exomes 𝑓: 0.31 (72631 hom.)
• Consequence: TAS1R2 NM_152232.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.90

Genes affected

TAS1R2 (HGNC:14905): (taste 1 receptor member 2) Contributes to sweet taste receptor activity. Involved in detection of chemical stimulus involved in sensory perception of sweet taste and positive regulation of cytokinesis. Part of sweet taste receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP7: Synonymous conserved (PhyloP=-4.9 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R2	NM_152232.6	c.882T>G	p.Thr294=	synonymous_variant	3/6	ENST00000375371.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R2	ENST00000375371.4	c.882T>G	p.Thr294=	synonymous_variant	3/6	2	NM_152232.6	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44011 AN: 152020 Hom.: 6593 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.300

GnomAD3 exomes AF: 0.285 AC: 71390 AN: 250748 Hom.: 10685 AF XY: 0.289 AC XY: 39154 AN XY: 135580

Gnomad AFR exome AF: 0.263

Gnomad AMR exome AF: 0.239

Gnomad ASJ exome AF: 0.332

Gnomad EAS exome AF: 0.105

Gnomad SAS exome AF: 0.284

Gnomad FIN exome AF: 0.292

Gnomad NFE exome AF: 0.324

Gnomad OTH exome AF: 0.314

GnomAD4 exome AF: 0.312 AC: 455779 AN: 1461594 Hom.: 72631 Cov.: 76 AF XY: 0.311 AC XY: 226247 AN XY: 727104

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.244

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.327

Gnomad4 OTH exome AF: 0.301

GnomAD4 genome AF: 0.289 AC: 44039 AN: 152138 Hom.: 6595 Cov.: 33 AF XY: 0.286 AC XY: 21258 AN XY: 74368

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.300

Alfa AF: 0.284 Hom.: 3301

Bravo AF: 0.288

Asia WGS AF: 0.193 AC: 671 AN: 3478

EpiCase AF: 0.332

EpiControl AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.25
Dann	Benign	0.49

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: rs28470550; hg19: chr1-19181082; COSMIC: COSV64744445;