rs28470550

Variant names:

• chr1-18854588-A-C
• rs28470550
• NM_152232.6:c.882T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-18854588-A-C
• chr1-18854588-A-G
• chr1-18854588-A-T

Variant summary

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

The NM_152232.6(TAS1R2):​c.882T>G​(p.Thr294Thr) 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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152232.6. 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
	TAS1R2	NM_152232.6	MANE Select	c.882T>G	p.Thr294Thr	synonymous	Exon 3 of 6	NP_689418.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R2	ENST00000375371.4	TSL:2 MANE Select	c.882T>G	p.Thr294Thr	synonymous	Exon 3 of 6	ENSP00000364520.3

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

GnomAD2 exomes AF: 0.285 AC: 71390 AN: 250748 AF XY: 0.289

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 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

African (AFR) AF: 0.260 AC: 8695 AN: 33478

American (AMR) AF: 0.244 AC: 10926 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 8660 AN: 26124

East Asian (EAS) AF: 0.119 AC: 4705 AN: 39694

South Asian (SAS) AF: 0.278 AC: 23991 AN: 86252

European-Finnish (FIN) AF: 0.290 AC: 15452 AN: 53276

Middle Eastern (MID) AF: 0.307 AC: 1773 AN: 5768

European-Non Finnish (NFE) AF: 0.327 AC: 363399 AN: 1111916

Other (OTH) AF: 0.301 AC: 18178 AN: 60384

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

African (AFR) AF: 0.261 AC: 10832 AN: 41510

American (AMR) AF: 0.268 AC: 4100 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3470

East Asian (EAS) AF: 0.106 AC: 547 AN: 5160

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4826

European-Finnish (FIN) AF: 0.280 AC: 2971 AN: 10592

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22074 AN: 67974

Other (OTH) AF: 0.300 AC: 635 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.49
PhyloP100		-4.9
Mutation Taster		=100/0	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: rs28470550; hg19: chr1-19181082; COSMIC: COSV64744445;