Genetic Variant TAS2R8:p.Leu183Leu (chr12-10806432-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_023918.3(TAS2R8):c.549G>A(p.Leu183Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,613,422 control chromosomes in the GnomAD database, including 279,485 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 21791 hom., cov: 31)

Exomes 𝑓: 0.59 ( 257694 hom. )

Consequence

TAS2R8
NM_023918.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0520

Publications

25 publications found

Variant links:

Genes affected

TAS2R8 (HGNC:14915): (taste 2 receptor member 8) 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]

TAS2R8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=0.052 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R8	NM_023918.3 link	c.549G>A	p.Leu183Leu	synonymous_variant	Exon 1 of 1	ENST00000240615.3	NP_076407.1	Q9NYW2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R8	ENST00000240615.3 link	c.549G>A	p.Leu183Leu	synonymous_variant	Exon 1 of 1	6	NM_023918.3	ENSP00000240615.2		Q9NYW2

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76739

AN:

151778

Hom.:

21807

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.851

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.664

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.599

Gnomad OTH

AF:

0.538

GnomAD2 exomes

AF:

0.590

AC:

147696

AN:

250312

AF XY:

0.598

show subpopulations

Gnomad AFR exome

AF:

0.220

Gnomad AMR exome

AF:

0.572

Gnomad ASJ exome

AF:

0.676

Gnomad EAS exome

AF:

0.664

Gnomad FIN exome

AF:

0.686

Gnomad NFE exome

AF:

0.608

Gnomad OTH exome

AF:

0.609

GnomAD4 exome

AF:

0.590

AC:

862460

AN:

1461526

Hom.:

257694

Cov.:

AF XY:

0.592

AC XY:

430468

AN XY:

727052

show subpopulations

African (AFR)

AF:

0.221

AC:

7408

AN:

33456

American (AMR)

AF:

0.573

AC:

25590

AN:

44656

Ashkenazi Jewish (ASJ)

AF:

0.680

AC:

17769

AN:

26122

East Asian (EAS)

AF:

0.668

AC:

26527

AN:

39684

South Asian (SAS)

AF:

0.591

AC:

50944

AN:

86242

European-Finnish (FIN)

AF:

0.681

AC:

36358

AN:

53378

Middle Eastern (MID)

AF:

0.639

AC:

3680

AN:

5762

European-Non Finnish (NFE)

AF:

0.593

AC:

659119

AN:

1111854

Other (OTH)

AF:

0.581

AC:

35065

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

21783

43566

65350

87133

108916

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17954

35908

53862

71816

89770

<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:

0.505

AC:

76728

AN:

151896

Hom.:

21791

Cov.:

AF XY:

0.512

AC XY:

37976

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.228

AC:

9451

AN:

41420

American (AMR)

AF:

0.569

AC:

8671

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.679

AC:

2355

AN:

3470

East Asian (EAS)

AF:

0.664

AC:

3420

AN:

5154

South Asian (SAS)

AF:

0.584

AC:

2815

AN:

4822

European-Finnish (FIN)

AF:

0.686

AC:

7246

AN:

10564

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.599

AC:

40673

AN:

67910

Other (OTH)

AF:

0.537

AC:

1133

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1705

3411

5116

6822

8527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

668

1336

2004

2672

3340

<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:

0.572

Hom.:

93080

Bravo

AF:

0.484

Asia WGS

AF:

0.591

AC:

2054

AN:

3478

EpiCase

AF:

0.614

EpiControl

AF:

0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

(source)

DANN

Benign

0.54

PhyloP100

0.052

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