dbSNP rs4726600: TAS2R39:c.*12G>A (chr7-143184447-G-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_176881.2(TAS2R39):c.*12G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,581,058 control chromosomes in the GnomAD database, including 43,166 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 0.17 ( 2998 hom., cov: 32)

Exomes 𝑓: 0.22 ( 40168 hom. )

Consequence

TAS2R39
NM_176881.2 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670

Publications

20 publications found

Variant links:

COSMIC-nc: COSV107531708

Genes affected

TAS2R39 (HGNC:18886): (taste 2 receptor member 39) The protein encoded by this gene is a bitter taste receptor that detects green tea catechins, soy isoflavones, and theaflavins. The encoded protein is gustducin-linked and may activate alpha gustducin. This gene is intronless. [provided by RefSeq, Dec 2015]

TAS2R39 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 (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R39	NM_176881.2 link	c.*12G>A		downstream_gene_variant		ENST00000446620.1	NP_795362.2	P59534

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R39	ENST00000446620.1 link	c.*12G>A		downstream_gene_variant		6	NM_176881.2	ENSP00000405095.1		P59534

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25576

AN:

151766

Hom.:

2997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0490

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0146

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.178

GnomAD2 exomes

AF:

0.173

AC:

36088

AN:

208340

AF XY:

0.175

show subpopulations

Gnomad AFR exome

AF:

0.0448

Gnomad AMR exome

AF:

0.109

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.0140

Gnomad FIN exome

AF:

0.280

Gnomad NFE exome

AF:

0.238

Gnomad OTH exome

AF:

0.190

GnomAD4 exome

AF:

0.220

AC:

314028

AN:

1429174

Hom.:

40168

Cov.:

AF XY:

0.217

AC XY:

153756

AN XY:

708534

show subpopulations

African (AFR)

AF:

0.0424

AC:

1390

AN:

32802

American (AMR)

AF:

0.112

AC:

4612

AN:

41260

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

4184

AN:

24036

East Asian (EAS)

AF:

0.0114

AC:

447

AN:

39360

South Asian (SAS)

AF:

0.103

AC:

8411

AN:

81562

European-Finnish (FIN)

AF:

0.278

AC:

13549

AN:

48804

Middle Eastern (MID)

AF:

0.113

AC:

635

AN:

5596

European-Non Finnish (NFE)

AF:

0.245

AC:

269067

AN:

1096706

Other (OTH)

AF:

0.199

AC:

11733

AN:

59048

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

11621

23242

34863

46484

58105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8822

17644

26466

35288

44110

<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:

0.168

AC:

25571

AN:

151884

Hom.:

2998

Cov.:

AF XY:

0.167

AC XY:

12419

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.0490

AC:

2030

AN:

41460

American (AMR)

AF:

0.157

AC:

2395

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

572

AN:

3462

East Asian (EAS)

AF:

0.0147

AC:

AN:

5186

South Asian (SAS)

AF:

0.101

AC:

485

AN:

4812

European-Finnish (FIN)

AF:

0.281

AC:

2963

AN:

10552

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16453

AN:

67862

Other (OTH)

AF:

0.176

AC:

369

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

993

1986

2980

3973

4966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.211

Hom.:

13143

Bravo

AF:

0.154

Asia WGS

AF:

0.0470

AC:

168

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

(source)

DANN

Benign

0.53

PhyloP100

-0.67

Mutation Taster

=81/19

polymorphism

(source)

Splicing

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