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GeneBe

7-122994789-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_016945.3(TAS2R16):c.846G>A(p.Thr282=) 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 (★).

Frequency

Genomes: 𝑓 0.11 ( 1904 hom., cov: 32)
Exomes 𝑓: 0.050 ( 2982 hom. )

Consequence

TAS2R16
NM_016945.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.196 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
TAS2R16NM_016945.3 linkuse as main transcriptc.846G>A p.Thr282= synonymous_variant 1/1 ENST00000249284.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAS2R16ENST00000249284.3 linkuse as main transcriptc.846G>A p.Thr282= synonymous_variant 1/1 NM_016945.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.112
AC:
17040
AN:
151842
Hom.:
1898
Cov.:
32
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.:
29
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.112
AC:
17061
AN:
151960
Hom.:
1904
Cov.:
32
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:
86
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

TAS2R16-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 20, 2019This 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.

Other links and lift over

dbSNP: rs1204014; hg19: chr7-122634843; COSMIC: COSV50796801; API