Variant 7-122995119-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016945.3(TAS2R16):c.516T>G(p.Asn172Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0153 in 1,613,670 control chromosomes in the GnomAD database, including 3,224 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Affects,risk factor (no stars).

Frequency

Genomes: 𝑓 0.081 ( 1688 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 1536 hom. )

Consequence

TAS2R16
NM_016945.3 missense

Scores

Clinical Significance

Affects; risk factor no assertion criteria provided O:2

Conservation

PhyloP100: -2.04

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0087378025).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS2R16	NM_016945.3 linkuse as main transcript	c.516T>G	p.Asn172Lys	missense_variant	1/1	ENST00000249284.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS2R16	ENST00000249284.3 linkuse as main transcript	c.516T>G	p.Asn172Lys	missense_variant	1/1		NM_016945.3	P1

Frequencies

GnomAD3 genomes

AF:

0.0810

AC:

12296

AN:

151880

Hom.:

1682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0267

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000830

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0382

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.0559

GnomAD3 exomes

AF:

0.0214

AC:

5362

AN:

250772

Hom.:

732

AF XY:

0.0157

AC XY:

2132

AN XY:

135494

show subpopulations

Gnomad AFR exome

AF:

0.290

Gnomad AMR exome

AF:

0.0133

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000555

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000936

Gnomad OTH exome

AF:

0.00999

GnomAD4 exome

AF:

0.00848

AC:

12395

AN:

1461672

Hom.:

1536

Cov.:

AF XY:

0.00731

AC XY:

5317

AN XY:

727140

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.0152

Gnomad4 ASJ exome

AF:

0.0000766

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000626

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000616

Gnomad4 OTH exome

AF:

0.0175

GnomAD4 genome

AF:

0.0810

AC:

12318

AN:

151998

Hom.:

1688

Cov.:

AF XY:

0.0772

AC XY:

5733

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.0266

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.0553

Alfa

AF:

0.0119

Hom.:

456

Bravo

AF:

0.0925

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.274

AC:

1206

ESP6500EA

AF:

0.00128

AC:

ExAC

AF:

0.0260

AC:

3152

Asia WGS

AF:

0.0170

AC:

AN:

3478

EpiCase

AF:

0.00180

EpiControl

AF:

0.00124

ClinVar

Significance: Affects; risk factor

Submissions summary: Other:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Alcohol dependence, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2007

- -

BETA-GLUCOPYRANOSIDE TASTING

Other:1

Affects, no assertion criteria provided

literature only

OMIM

Feb 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

Cadd

Benign

0.17

Dann

Benign

0.089

DEOGEN2

Benign

0.0067

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00091

LIST_S2

Benign

0.20

MetaRNN

Benign

0.0087

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

MutationTaster

Benign

1.0

PrimateAI

Benign

0.24

PROVEAN

Benign

0.31

REVEL

Benign

0.026

Sift

Benign

0.94

Sift4G

Benign

0.96

Polyphen

0.0

Vest4

0.026

MutPred

0.14

Gain of methylation at N172 (P = 0.0039);

MPC

0.011

ClinPred

0.0020

GERP RS

-3.5

Varity_R

0.038

gMVP

0.053

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

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