NM_176889.4:c.764G>T

Variant names:

Variant summary

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

The NM_176889.4(TAS2R20):c.764G>T(p.Arg255Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,612,704 control chromosomes in the GnomAD database, including 113,653 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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 0.30 ( 8846 hom., cov: 32)

Exomes 𝑓: 0.36 ( 104807 hom. )

Consequence

TAS2R20
NM_176889.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.885

Publications

41 publications found

Variant links:

Genes affected

TAS2R20 (HGNC:19109): (taste 2 receptor member 20) This gene encodes a member of the taste receptor two family of class C G-protein coupled receptors. Receptors of this family have a short extracellular N-terminus, seven transmembrane helices, three extracellular loops and three intracellular loops, and an intracellular C-terminus. Members of this family are expressed in a subset of taste receptor cells, where they function in bitter taste reception, as well as in non-gustatory cells including those of the brain, reproductive organs, respiratory system, and gastrointestinal system. This gene maps to the taste receptor gene cluster on chromosome 12p13. [provided by RefSeq, Jul 2016]

TAS2R20 links:

ENSG00000275778 (HGNC:):

ENSG00000275778 links:

PRH1 (HGNC:9366): (proline rich protein HaeIII subfamily 1) This gene encodes a member of the heterogeneous family of proline-rich salivary glycoproteins. The encoded preproprotein undergoes proteolytic processing to generate one or more mature isoforms before secretion from the parotid and submandibular/sublingual glands. Multiple distinct alleles of this locus including the parotid isoelectric-focusing variant slow (PIF-s), the parotid acidic protein (Pa), and the double band slow (Db-s) isoforms have been characterized. The reference genome encodes the Db-s allele. Certain alleles of this gene are associated with susceptibility to dental caries. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. Co-transcription of this gene with adjacent genes has been observed. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

PRH1 links:

PRR4 (HGNC:18020): (proline rich 4) This gene encodes a member of the proline-rich protein family that lacks a conserved repetitive domain. This protein may play a role in protective functions in the eye. Alternative splicing result in multiple transcript variants. Read-through transcription also exists between this gene and the upstream PRH1 (proline-rich protein HaeIII subfamily 1) gene. [provided by RefSeq, Feb 2011]

PRR4 links:

TAS2R14 (HGNC:14920): (taste 2 receptor member 14) This gene product belongs to the family of candidate taste receptors that are members of the G-protein-coupled receptor superfamily. These proteins are specifically expressed in the taste receptor cells of the tongue and palate epithelia. They are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. In functional expression studies, they respond to bitter tastants. This gene maps to the taste receptor gene cluster on chromosome 12p13. [provided by RefSeq, Jul 2008]

TAS2R14 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=5.843094E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R20	NM_176889.4 link	c.764G>T	p.Arg255Leu	missense_variant	Exon 1 of 1	ENST00000538986.2	NP_795370.2	P59543

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R20	ENST00000538986.2 link	c.764G>T	p.Arg255Leu	missense_variant	Exon 1 of 1	6	NM_176889.4	ENSP00000441624.1		P59543
ENSG00000275778	ENST00000536668.2 link	n.110-23391G>T		intron_variant	Intron 3 of 9	5		ENSP00000482961.1		A0A087WZY1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46162

AN:

151686

Hom.:

8842

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.393

Gnomad ASJ

AF:

0.528

Gnomad EAS

AF:

0.735

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.328

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.360

GnomAD2 exomes

AF:

0.416

AC:

104409

AN:

250982

AF XY:

0.430

show subpopulations

Gnomad AFR exome

AF:

0.0975

Gnomad AMR exome

AF:

0.452

Gnomad ASJ exome

AF:

0.518

Gnomad EAS exome

AF:

0.751

Gnomad FIN exome

AF:

0.330

Gnomad NFE exome

AF:

0.347

Gnomad OTH exome

AF:

0.403

GnomAD4 exome

AF:

0.361

AC:

527836

AN:

1460898

Hom.:

104807

Cov.:

AF XY:

0.371

AC XY:

269302

AN XY:

726798

show subpopulations

African (AFR)

AF:

0.0976

AC:

3266

AN:

33470

American (AMR)

AF:

0.446

AC:

19950

AN:

44692

Ashkenazi Jewish (ASJ)

AF:

0.528

AC:

13783

AN:

26128

East Asian (EAS)

AF:

0.749

AC:

29707

AN:

39688

South Asian (SAS)

AF:

0.617

AC:

53168

AN:

86208

European-Finnish (FIN)

AF:

0.324

AC:

17315

AN:

53412

Middle Eastern (MID)

AF:

0.555

AC:

3198

AN:

5764

European-Non Finnish (NFE)

AF:

0.328

AC:

364145

AN:

1111182

Other (OTH)

AF:

0.386

AC:

23304

AN:

60354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

18248

36496

54743

72991

91239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11900

23800

35700

47600

59500

<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:

0.304

AC:

46177

AN:

151806

Hom.:

8846

Cov.:

AF XY:

0.314

AC XY:

23292

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.106

AC:

4404

AN:

41472

American (AMR)

AF:

0.393

AC:

5986

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.528

AC:

1830

AN:

3468

East Asian (EAS)

AF:

0.735

AC:

3767

AN:

5126

South Asian (SAS)

AF:

0.622

AC:

2988

AN:

4806

European-Finnish (FIN)

AF:

0.328

AC:

3442

AN:

10504

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22627

AN:

67888

Other (OTH)

AF:

0.364

AC:

767

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1532

3064

4596

6128

7660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.354

Hom.:

34730

Bravo

AF:

0.301

TwinsUK

AF:

0.319

AC:

1181

ALSPAC

AF:

0.317

AC:

1220

ESP6500AA

AF:

0.100

AC:

442

ESP6500EA

AF:

0.351

AC:

3016

ExAC

AF:

0.411

AC:

49914

Asia WGS

AF:

0.608

AC:

2109

AN:

3478

EpiCase

AF:

0.366

EpiControl

AF:

0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.86

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.0030

(source)

DANN

Benign

0.41

DEOGEN2

Benign

0.00025

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.00072

MetaRNN

Benign

0.0000058

MetaSVM

Benign

-0.92

MutationAssessor

Benign

-2.2

PhyloP100

-0.89

PrimateAI

Benign

0.23

PROVEAN

Benign

2.0

REVEL

Benign

0.047

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.023

MPC

0.025

ClinPred

0.0031

GERP RS

-5.3

Varity_R

0.047

gMVP

0.034

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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