dbSNP rs10260248: TAS2R40:p.Ser187Tyr (chr7-143222638-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_176882.2(TAS2R40):c.560C>A(p.Ser187Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 1,614,064 control chromosomes in the GnomAD database, including 3,929 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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 0.084 ( 637 hom., cov: 32)

Exomes 𝑓: 0.063 ( 3292 hom. )

Consequence

TAS2R40
NM_176882.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851

Publications

19 publications found

Variant links:

Genes affected

TAS2R40 (HGNC:18885): (taste 2 receptor member 40) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. A decrease in the expression of this gene is associated with hypogeusia. [provided by RefSeq, Jul 2017]

TAS2R40 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0015716851).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R40	NM_176882.2 link	c.560C>A	p.Ser187Tyr	missense_variant	Exon 1 of 1	ENST00000408947.4	NP_795363.1	P59535

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R40	ENST00000408947.4 link	c.560C>A	p.Ser187Tyr	missense_variant	Exon 1 of 1	6	NM_176882.2	ENSP00000386210.3		P59535

Frequencies

GnomAD3 genomes

AF:

0.0841

AC:

12783

AN:

152084

Hom.:

637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.0556

Gnomad EAS

AF:

0.0251

Gnomad SAS

AF:

0.0958

Gnomad FIN

AF:

0.0305

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0628

Gnomad OTH

AF:

0.0703

GnomAD2 exomes

AF:

0.0680

AC:

16945

AN:

249214

AF XY:

0.0679

show subpopulations

Gnomad AFR exome

AF:

0.144

Gnomad AMR exome

AF:

0.0739

Gnomad ASJ exome

AF:

0.0541

Gnomad EAS exome

AF:

0.0262

Gnomad FIN exome

AF:

0.0294

Gnomad NFE exome

AF:

0.0640

Gnomad OTH exome

AF:

0.0592

GnomAD4 exome

AF:

0.0632

AC:

92390

AN:

1461862

Hom.:

3292

Cov.:

AF XY:

0.0639

AC XY:

46483

AN XY:

727238

show subpopulations

African (AFR)

AF:

0.143

AC:

4782

AN:

33478

American (AMR)

AF:

0.0740

AC:

3311

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0544

AC:

1423

AN:

26136

East Asian (EAS)

AF:

0.0192

AC:

764

AN:

39700

South Asian (SAS)

AF:

0.0963

AC:

8307

AN:

86258

European-Finnish (FIN)

AF:

0.0298

AC:

1590

AN:

53412

Middle Eastern (MID)

AF:

0.0777

AC:

448

AN:

5768

European-Non Finnish (NFE)

AF:

0.0611

AC:

67944

AN:

1111992

Other (OTH)

AF:

0.0633

AC:

3821

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

5701

11401

17102

22802

28503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0841

AC:

12793

AN:

152202

Hom.:

637

Cov.:

AF XY:

0.0815

AC XY:

6066

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.147

AC:

6118

AN:

41528

American (AMR)

AF:

0.0696

AC:

1064

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0556

AC:

193

AN:

3470

East Asian (EAS)

AF:

0.0252

AC:

130

AN:

5166

South Asian (SAS)

AF:

0.0967

AC:

466

AN:

4818

European-Finnish (FIN)

AF:

0.0305

AC:

323

AN:

10606

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0628

AC:

4273

AN:

68004

Other (OTH)

AF:

0.0695

AC:

147

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

582

1164

1747

2329

2911

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0683

Hom.:

1673

Bravo

AF:

0.0893

TwinsUK

AF:

0.0561

AC:

208

ALSPAC

AF:

0.0659

AC:

254

ESP6500AA

AF:

0.134

AC:

509

ESP6500EA

AF:

0.0594

AC:

491

ExAC

AF:

0.0711

AC:

8593

Asia WGS

AF:

0.0560

AC:

197

AN:

3478

EpiCase

AF:

0.0634

EpiControl

AF:

0.0684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.099

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.20

DEOGEN2

Benign

0.0043

Eigen

Benign

-0.10

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.80

MetaRNN

Benign

0.0016

MetaSVM

Benign

-0.90

MutationAssessor

Uncertain

2.4

PhyloP100

-0.85

PrimateAI

Benign

0.26

PROVEAN

Uncertain

-2.8

REVEL

Benign

0.081

Sift

Benign

0.93

Sift4G

Uncertain

0.050

Polyphen

0.76

Vest4

0.058

MPC

0.16

ClinPred

0.062

GERP RS

2.1

Varity_R

0.11

gMVP

0.17

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

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rs10260248

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