dbSNP rs35874116: TAS1R2:p.Ile191Val (chr1-18854899-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152232.6(TAS1R2):c.571A>G(p.Ile191Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,612,726 control chromosomes in the GnomAD database, including 83,033 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 7487 hom., cov: 33)

Exomes 𝑓: 0.32 ( 75546 hom. )

Consequence

TAS1R2
NM_152232.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486

Publications

68 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.0253353E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6 link	c.571A>G	p.Ile191Val	missense_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.571A>G	p.Ile191Val	missense_variant	Exon 3 of 6	2	NM_152232.6	ENSP00000364520.3		Q8TE23

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

47010

AN:

152022

Hom.:

7484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.277

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.314

GnomAD2 exomes

AF:

0.294

AC:

73268

AN:

249498

AF XY:

0.298

show subpopulations

Gnomad AFR exome

AF:

0.323

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.332

Gnomad EAS exome

AF:

0.106

Gnomad FIN exome

AF:

0.293

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.318

AC:

464945

AN:

1460586

Hom.:

75546

Cov.:

AF XY:

0.318

AC XY:

230784

AN XY:

726462

show subpopulations

African (AFR)

AF:

0.322

AC:

10761

AN:

33454

American (AMR)

AF:

0.248

AC:

11096

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

8659

AN:

26124

East Asian (EAS)

AF:

0.119

AC:

4723

AN:

39688

South Asian (SAS)

AF:

0.295

AC:

25479

AN:

86252

European-Finnish (FIN)

AF:

0.290

AC:

15267

AN:

52686

Middle Eastern (MID)

AF:

0.315

AC:

1814

AN:

5766

European-Non Finnish (NFE)

AF:

0.331

AC:

368468

AN:

1111568

Other (OTH)

AF:

0.309

AC:

18678

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

19397

38793

58190

77586

96983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11924

23848

35772

47696

59620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.309

AC:

47046

AN:

152140

Hom.:

7487

Cov.:

AF XY:

0.305

AC XY:

22663

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.321

AC:

13308

AN:

41494

American (AMR)

AF:

0.277

AC:

4230

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1186

AN:

3472

East Asian (EAS)

AF:

0.107

AC:

553

AN:

5178

South Asian (SAS)

AF:

0.266

AC:

1285

AN:

4822

European-Finnish (FIN)

AF:

0.281

AC:

2978

AN:

10604

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.329

AC:

22358

AN:

67968

Other (OTH)

AF:

0.314

AC:

664

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1743

3486

5228

6971

8714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.319

Hom.:

19494

Bravo

AF:

0.310

TwinsUK

AF:

0.334

AC:

1239

ALSPAC

AF:

0.326

AC:

1255

ESP6500AA

AF:

0.306

AC:

1349

ESP6500EA

AF:

0.331

AC:

2845

ExAC

AF:

0.299

AC:

36323

Asia WGS

AF:

0.211

AC:

736

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

0.024

(source)

DANN

Benign

0.34

DEOGEN2

Benign

0.044

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.039

LIST_S2

Benign

0.46

MetaRNN

Benign

0.00090

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.20

PhyloP100

-0.49

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.11

REVEL

Benign

0.21

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.033

MPC

0.10

ClinPred

0.0022

GERP RS

-4.1

Varity_R

0.022

gMVP

0.36

Mutation Taster

=94/6

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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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