Genetic Variant TAS1R2:p.Ser9Cys (chr1-18859635-G-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.26C>G(p.Ser9Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,614,024 control chromosomes in the GnomAD database, including 494,997 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 0.79 ( 47250 hom., cov: 34)

Exomes 𝑓: 0.78 ( 447747 hom. )

Consequence

TAS1R2
NM_152232.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200

Publications

43 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=1.7540721E-6).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6 link	c.26C>G	p.Ser9Cys	missense_variant	Exon 1 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.26C>G	p.Ser9Cys	missense_variant	Exon 1 of 6	2	NM_152232.6	ENSP00000364520.3		Q8TE23

Frequencies

GnomAD3 genomes

AF:

0.787

AC:

119762

AN:

152136

Hom.:

47218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.873

Gnomad AMR

AF:

0.828

Gnomad ASJ

AF:

0.816

Gnomad EAS

AF:

0.757

Gnomad SAS

AF:

0.798

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.773

Gnomad OTH

AF:

0.814

GnomAD2 exomes

AF:

0.782

AC:

196556

AN:

251376

AF XY:

0.781

show subpopulations

Gnomad AFR exome

AF:

0.815

Gnomad AMR exome

AF:

0.830

Gnomad ASJ exome

AF:

0.817

Gnomad EAS exome

AF:

0.758

Gnomad FIN exome

AF:

0.691

Gnomad NFE exome

AF:

0.778

Gnomad OTH exome

AF:

0.782

GnomAD4 exome

AF:

0.782

AC:

1142576

AN:

1461770

Hom.:

447747

Cov.:

AF XY:

0.781

AC XY:

568299

AN XY:

727206

show subpopulations

African (AFR)

AF:

0.820

AC:

27445

AN:

33474

American (AMR)

AF:

0.832

AC:

37219

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.819

AC:

21401

AN:

26136

East Asian (EAS)

AF:

0.717

AC:

28483

AN:

39698

South Asian (SAS)

AF:

0.792

AC:

68333

AN:

86254

European-Finnish (FIN)

AF:

0.688

AC:

36763

AN:

53414

Middle Eastern (MID)

AF:

0.815

AC:

4703

AN:

5768

European-Non Finnish (NFE)

AF:

0.783

AC:

870924

AN:

1111916

Other (OTH)

AF:

0.783

AC:

47305

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

14200

28400

42600

56800

71000

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.787

AC:

119842

AN:

152254

Hom.:

47250

Cov.:

AF XY:

0.783

AC XY:

58268

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.817

AC:

33940

AN:

41528

American (AMR)

AF:

0.828

AC:

12674

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.816

AC:

2833

AN:

3472

East Asian (EAS)

AF:

0.756

AC:

3906

AN:

5166

South Asian (SAS)

AF:

0.799

AC:

3854

AN:

4824

European-Finnish (FIN)

AF:

0.686

AC:

7281

AN:

10616

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.773

AC:

52588

AN:

68018

Other (OTH)

AF:

0.817

AC:

1728

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1347

2694

4040

5387

6734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.781

Hom.:

34988

Bravo

AF:

0.800

TwinsUK

AF:

0.785

AC:

2912

ALSPAC

AF:

0.791

AC:

3047

ESP6500AA

AF:

0.830

AC:

3658

ESP6500EA

AF:

0.773

AC:

6650

ExAC

AF:

0.780

AC:

94744

Asia WGS

AF:

0.764

AC:

2658

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.046

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

0.34

(source)

DANN

Benign

0.56

DEOGEN2

Benign

0.016

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0017

LIST_S2

Benign

0.18

MetaRNN

Benign

0.0000018

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-2.7

PhyloP100

-0.020

PrimateAI

Benign

0.37

PROVEAN

Benign

2.0

REVEL

Benign

0.15

Sift

Benign

1.0

Sift4G

Benign

0.42

Polyphen

0.0

Vest4

0.029

MPC

0.12

ClinPred

0.0063

GERP RS

1.1

PromoterAI

-0.021

Neutral

(source)

Varity_R

0.062

gMVP

0.59

Mutation Taster

=99/1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

1-18859635-G-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