Genetic Variant NM_016945.3:c.846G>A (chr7-122994789-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_016945.3(TAS2R16):c.846G>A(p.Thr282Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 1,591,196 control chromosomes in the GnomAD database, including 4,886 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.11 ( 1904 hom., cov: 32)

Exomes 𝑓: 0.050 ( 2982 hom. )

Consequence

TAS2R16
NM_016945.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.196

Publications

12 publications found

Variant links:

Genes affected

TAS2R16 (HGNC:14921): (taste 2 receptor member 16) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily. These family members are specifically expressed by taste receptor cells of the tongue and palate epithelia. Each of these apparently intronless genes encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes in chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

TAS2R16 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 7-122994789-C-T is Benign according to our data. Variant chr7-122994789-C-T is described in ClinVar as Benign. ClinVar VariationId is 3055321.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.196 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R16	NM_016945.3 link	c.846G>A	p.Thr282Thr	synonymous_variant	Exon 1 of 1	ENST00000249284.3	NP_058641.1	Q9NYV7A0A8E5KFD5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R16	ENST00000249284.3 link	c.846G>A	p.Thr282Thr	synonymous_variant	Exon 1 of 1	6	NM_016945.3	ENSP00000249284.2		Q9NYV7

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17040

AN:

151842

Hom.:

1898

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.000388

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.0630

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0468

Gnomad OTH

AF:

0.0755

GnomAD2 exomes

AF:

0.0545

AC:

12552

AN:

230184

AF XY:

0.0494

show subpopulations

Gnomad AFR exome

AF:

0.297

Gnomad AMR exome

AF:

0.0312

Gnomad ASJ exome

AF:

0.00974

Gnomad EAS exome

AF:

0.000112

Gnomad FIN exome

AF:

0.0620

Gnomad NFE exome

AF:

0.0468

Gnomad OTH exome

AF:

0.0415

GnomAD4 exome

AF:

0.0497

AC:

71503

AN:

1439236

Hom.:

2982

Cov.:

AF XY:

0.0478

AC XY:

34171

AN XY:

714636

show subpopulations

African (AFR)

AF:

0.300

AC:

9772

AN:

32572

American (AMR)

AF:

0.0341

AC:

1416

AN:

41536

Ashkenazi Jewish (ASJ)

AF:

0.00986

AC:

237

AN:

24038

East Asian (EAS)

AF:

0.000126

AC:

AN:

39622

South Asian (SAS)

AF:

0.0155

AC:

1263

AN:

81634

European-Finnish (FIN)

AF:

0.0653

AC:

3422

AN:

52390

Middle Eastern (MID)

AF:

0.0229

AC:

128

AN:

5598

European-Non Finnish (NFE)

AF:

0.0473

AC:

52129

AN:

1102536

Other (OTH)

AF:

0.0528

AC:

3131

AN:

59310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

3830

7659

11489

15318

19148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2048

4096

6144

8192

10240

<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:

0.112

AC:

17061

AN:

151960

Hom.:

1904

Cov.:

AF XY:

0.109

AC XY:

8096

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.291

AC:

12038

AN:

41414

American (AMR)

AF:

0.0551

AC:

842

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0107

AC:

AN:

3468

East Asian (EAS)

AF:

0.000389

AC:

AN:

5144

South Asian (SAS)

AF:

0.0112

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0630

AC:

666

AN:

10576

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0468

AC:

3180

AN:

67946

Other (OTH)

AF:

0.0743

AC:

157

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

661

1322

1983

2644

3305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.0776

Hom.:

1838

Bravo

AF:

0.119

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TAS2R16-related disorder

Benign:1

Nov 20, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.0

(source)

DANN

Benign

0.51

PhyloP100

-0.20

Mutation Taster

=100/0

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over