rs12033832

Positions:

• chr1-18839800-G-A
• chr1-18839800-G-C

Variant summary

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

The NM_152232.6(TAS1R2):​c.2319C>T​(p.Ser773Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,613,942 control chromosomes in the GnomAD database, including 90,178 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 0.30 (6986 hom., cov: 33)
  • Exomes 𝑓: 0.33 (83192 hom.)
• Consequence: TAS1R2 NM_152232.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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=-0.78).
• BP7: Synonymous conserved (PhyloP=0.102 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.2319C>T	p.Ser773Ser	synonymous_variant	6/6	ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.2319C>T	p.Ser773Ser	synonymous_variant	6/6	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45042 AN: 152044 Hom.: 6985 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.285

GnomAD3 exomes AF: 0.309 AC: 77680 AN: 251166 Hom.: 12642 AF XY: 0.311 AC XY: 42281 AN XY: 135764

Gnomad AFR exome AF: 0.231

Gnomad AMR exome AF: 0.236

Gnomad ASJ exome AF: 0.241

Gnomad EAS exome AF: 0.454

Gnomad SAS exome AF: 0.266

Gnomad FIN exome AF: 0.313

Gnomad NFE exome AF: 0.337

Gnomad OTH exome AF: 0.306

GnomAD4 exome AF: 0.334 AC: 487779 AN: 1461780 Hom.: 83192 Cov.: 77 AF XY: 0.332 AC XY: 241320 AN XY: 727194

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.243

Gnomad4 EAS exome AF: 0.466

Gnomad4 SAS exome AF: 0.270

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.322

GnomAD4 genome AF: 0.296 AC: 45066 AN: 152162 Hom.: 6986 Cov.: 33 AF XY: 0.293 AC XY: 21823 AN XY: 74396

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.282

Alfa AF: 0.312 Hom.: 4164

Bravo AF: 0.290

Asia WGS AF: 0.343 AC: 1194 AN: 3478

EpiCase AF: 0.333

EpiControl AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.9
DANN	Benign	0.57

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: rs12033832; hg19: chr1-19166294; COSMIC: COSV64744719;