Genetic Variant TAS1R2:p.Thr294Thr (chr1-18854588-A-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.90

Publications

9 publications found

Variant links:

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]

TAS1R2 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6 link	c.882T>G	p.Thr294Thr	synonymous_variant	Exon 3 of 6	ENST00000375371.4	NP_689418.2	Q8TE23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4 link	c.882T>G	p.Thr294Thr	synonymous_variant	Exon 3 of 6	2	NM_152232.6	ENSP00000364520.3		Q8TE23

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44011

AN:

152020

Hom.:

6593

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.311

AC XY:

226247

AN XY:

727104

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

22585

45170

67754

90339

112924

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.289

AC:

44039

AN:

152138

Hom.:

6595

Cov.:

AF XY:

0.286

AC XY:

21258

AN XY:

74368

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1681

3363

5044

6726

8407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

(source)

DANN

Benign

0.49

PhyloP100

-4.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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1-18854588-A-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over