Variant 7-122994789-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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/exons	MANE	Protein	UniProt
TAS2R16	NM_016945.3 linkuse as main transcript	c.846G>A	p.Thr282Thr	synonymous_variant	1/1	ENST00000249284.3	NP_058641.1	Q9NYV7A0A8E5KFD5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R16	ENST00000249284.3 linkuse as main transcript	c.846G>A	p.Thr282Thr	synonymous_variant	1/1	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

GnomAD3 exomes

AF:

0.0545

AC:

12552

AN:

230184

Hom.:

930

AF XY:

0.0494

AC XY:

6110

AN XY:

123786

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 SAS exome

AF:

0.0135

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

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.0341

Gnomad4 ASJ exome

AF:

0.00986

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0155

Gnomad4 FIN exome

AF:

0.0653

Gnomad4 NFE exome

AF:

0.0473

Gnomad4 OTH exome

AF:

0.0528

GnomAD4 genome

AF:

0.112

AC:

17061

AN:

151960

Hom.:

1904

Cov.:

AF XY:

0.109

AC XY:

8096

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.0551

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.000389

Gnomad4 SAS

AF:

0.0112

Gnomad4 FIN

AF:

0.0630

Gnomad4 NFE

AF:

0.0468

Gnomad4 OTH

AF:

0.0743

Alfa

AF:

0.0831

Hom.:

499

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

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 20, 2019

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

DANN

Benign

0.51

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over