dbSNP rs10278721: TAS2R41:p.Pro127Leu (chr7-143478252-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_176883.2(TAS2R41):c.380C>T(p.Pro127Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,772 control chromosomes in the GnomAD database, including 60,758 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 0.22 ( 4414 hom., cov: 30)

Exomes 𝑓: 0.27 ( 56344 hom. )

Consequence

TAS2R41
NM_176883.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

Publications

33 publications found

Variant links:

Genes affected

TAS2R41 (HGNC:18883): (taste 2 receptor member 41) 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. Chloramphenicol is an agonist for the encoded protein. [provided by RefSeq, Jul 2017]

TAS2R41 links:

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

EPHA1-AS1 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=0.004470557).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R41	NM_176883.2 link	c.380C>T	p.Pro127Leu	missense_variant	Exon 1 of 1	ENST00000408916.1	NP_795364.2
EPHA1-AS1	NR_033897.1 link	n.207-26522C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R41	ENST00000408916.1 link	c.380C>T	p.Pro127Leu	missense_variant	Exon 1 of 1	6	NM_176883.2	ENSP00000386201.1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33213

AN:

151858

Hom.:

4405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0593

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.232

GnomAD2 exomes

AF:

0.266

AC:

66216

AN:

249162

AF XY:

0.270

show subpopulations

Gnomad AFR exome

AF:

0.0557

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.274

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.275

AC:

401655

AN:

1461796

Hom.:

56344

Cov.:

AF XY:

0.277

AC XY:

201114

AN XY:

727204

show subpopulations

African (AFR)

AF:

0.0509

AC:

1703

AN:

33480

American (AMR)

AF:

0.289

AC:

12931

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

6620

AN:

26136

East Asian (EAS)

AF:

0.315

AC:

12496

AN:

39698

South Asian (SAS)

AF:

0.316

AC:

27287

AN:

86254

European-Finnish (FIN)

AF:

0.269

AC:

14354

AN:

53396

Middle Eastern (MID)

AF:

0.200

AC:

1152

AN:

5768

European-Non Finnish (NFE)

AF:

0.278

AC:

309116

AN:

1111952

Other (OTH)

AF:

0.265

AC:

15996

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

18588

37177

55765

74354

92942

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10260

20520

30780

41040

51300

<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:

0.219

AC:

33237

AN:

151976

Hom.:

4414

Cov.:

AF XY:

0.222

AC XY:

16520

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.0594

AC:

2462

AN:

41474

American (AMR)

AF:

0.282

AC:

4307

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

901

AN:

3470

East Asian (EAS)

AF:

0.290

AC:

1491

AN:

5140

South Asian (SAS)

AF:

0.321

AC:

1545

AN:

4810

European-Finnish (FIN)

AF:

0.266

AC:

2804

AN:

10554

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

19059

AN:

67954

Other (OTH)

AF:

0.231

AC:

487

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1239

2478

3717

4956

6195

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.257

Hom.:

15756

Bravo

AF:

0.209

TwinsUK

AF:

0.261

AC:

967

ALSPAC

AF:

0.279

AC:

1076

ESP6500AA

AF:

0.0595

AC:

232

ESP6500EA

AF:

0.273

AC:

2266

ExAC

AF:

0.262

AC:

31650

Asia WGS

AF:

0.273

AC:

951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0090

Eigen

Benign

-0.47

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.039

MetaRNN

Benign

0.0045

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.9

PhyloP100

0.0010

PrimateAI

Benign

0.31

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.087

Sift

Benign

0.066

Sift4G

Benign

0.085

Polyphen

0.42

Vest4

0.11

MPC

0.12

ClinPred

0.025

GERP RS

1.5

PromoterAI

0.011

Neutral

(source)

Varity_R

0.11

gMVP

0.15

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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