rs3741845

Variant names:

• chr12-10809516-A-G
• rs3741845
• NM_023917.2:c.560T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_023917.2(TAS2R9):​c.560T>C​(p.Val187Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 1,612,848 control chromosomes in the GnomAD database, including 289,540 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

• Frequency:
  • Genomes: 𝑓 0.52 (22804 hom., cov: 29)
  • Exomes 𝑓: 0.60 (266736 hom.)
• Consequence: TAS2R9 NM_023917.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44

Genes affected

TAS2R9 (HGNC:14917): (taste 2 receptor member 9) This gene product belongs to the family of candidate taste receptors that are members of the G-protein-coupled receptor superfamily. These proteins are specifically expressed in the taste receptor cells of the tongue and palate epithelia. They are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. In functional expression studies, they respond to bitter tastants. This gene maps to the taste receptor gene cluster on chromosome 12p13. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=4.819567E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R9	NM_023917.2	c.560T>C	p.Val187Ala	missense_variant	Exon 1 of 1	ENST00000240691.4	NP_076406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R9	ENST00000240691.4	c.560T>C	p.Val187Ala	missense_variant	Exon 1 of 1	6	NM_023917.2	ENSP00000240691.2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 78951 AN: 151300 Hom.: 22815 Cov.: 29

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.552

GnomAD2 exomes AF: 0.603 AC: 150804 AN: 250170 AF XY: 0.610

Gnomad AFR exome AF: 0.251

Gnomad AMR exome AF: 0.578

Gnomad ASJ exome AF: 0.679

Gnomad EAS exome AF: 0.725

Gnomad FIN exome AF: 0.688

Gnomad NFE exome AF: 0.617

Gnomad OTH exome AF: 0.622

GnomAD4 exome AF: 0.601 AC: 877800 AN: 1461430 Hom.: 266736 Cov.: 65 AF XY: 0.602 AC XY: 437894 AN XY: 726996

Gnomad4 AFR exome AF: 0.251 AC: 8407 AN: 33456

Gnomad4 AMR exome AF: 0.580 AC: 25873 AN: 44610

Gnomad4 ASJ exome AF: 0.683 AC: 17839 AN: 26110

Gnomad4 EAS exome AF: 0.713 AC: 28314 AN: 39688

Gnomad4 SAS exome AF: 0.597 AC: 51494 AN: 86238

Gnomad4 FIN exome AF: 0.684 AC: 36515 AN: 53398

Gnomad4 NFE exome AF: 0.602 AC: 669778 AN: 1111798

Gnomad4 Remaining exome AF: 0.594 AC: 35840 AN: 60376

GnomAD4 genome AF: 0.521 AC: 78963 AN: 151418 Hom.: 22804 Cov.: 29 AF XY: 0.527 AC XY: 38960 AN XY: 73926

Gnomad4 AFR AF: 0.258 AC: 0.257922 AN: 0.257922

Gnomad4 AMR AF: 0.580 AC: 0.579752 AN: 0.579752

Gnomad4 ASJ AF: 0.682 AC: 0.681949 AN: 0.681949

Gnomad4 EAS AF: 0.725 AC: 0.724558 AN: 0.724558

Gnomad4 SAS AF: 0.592 AC: 0.592215 AN: 0.592215

Gnomad4 FIN AF: 0.686 AC: 0.686244 AN: 0.686244

Gnomad4 NFE AF: 0.609 AC: 0.608661 AN: 0.608661

Gnomad4 OTH AF: 0.553 AC: 0.553181 AN: 0.553181

Alfa AF: 0.578 Hom.: 48457

Bravo AF: 0.502

TwinsUK AF: 0.604 AC: 2238

ALSPAC AF: 0.597 AC: 2301

ESP6500AA AF: 0.261 AC: 1148

ESP6500EA AF: 0.613 AC: 5268

ExAC AF: 0.596 AC: 72312

Asia WGS AF: 0.635 AC: 2207 AN: 3478

EpiCase AF: 0.623

EpiControl AF: 0.617

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.82	T
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.0050
DANN	Benign	0.45
DEOGEN2	Benign	0.0022	T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.2
FATHMM_MKL	Benign	0.0022	N
MetaRNN	Benign	0.0000048	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.47	N
PrimateAI	Benign	0.22	T
PROVEAN	Benign	1.2	N
REVEL	Benign	0.020
Sift	Benign	0.91	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.0060
MPC		0.0081
ClinPred		0.0079	T
GERP RS		-3.4
Varity_R		0.024
gMVP		0.029
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3741845; hg19: chr12-10962115; COSMIC: COSV53688249; COSMIC: COSV53688249;