NM_152232.6:c.2319C>T

Variant names:

• chr1-18839800-G-A
• rs12033832
• NM_152232.6:c.2319C>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.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
• Publications: 25 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=-0.78).
• 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.

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.2319C>T	p.Ser773Ser	synonymous	Exon 6 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.2319C>T	p.Ser773Ser	synonymous	Exon 6 of 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

GnomAD2 exomes AF: 0.309 AC: 77680 AN: 251166 AF XY: 0.311

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 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

African (AFR) AF: 0.227 AC: 7607 AN: 33480

American (AMR) AF: 0.240 AC: 10724 AN: 44700

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 6345 AN: 26134

East Asian (EAS) AF: 0.466 AC: 18500 AN: 39698

South Asian (SAS) AF: 0.270 AC: 23305 AN: 86254

European-Finnish (FIN) AF: 0.317 AC: 16953 AN: 53418

Middle Eastern (MID) AF: 0.239 AC: 1380 AN: 5768

European-Non Finnish (NFE) AF: 0.345 AC: 383521 AN: 1111940

Other (OTH) AF: 0.322 AC: 19444 AN: 60388

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

African (AFR) AF: 0.236 AC: 9805 AN: 41524

American (AMR) AF: 0.259 AC: 3965 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2298 AN: 5164

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3268 AN: 10586

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22717 AN: 67980

Other (OTH) AF: 0.282 AC: 596 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.10
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: rs12033832; hg19: chr1-19166294; COSMIC: COSV64744719;