rs2233989

Positions:

• chr7-122995175-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_016945.3(TAS2R16):​c.460T>C​(p.Leu154Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00637 in 1,613,810 control chromosomes in the GnomAD database, including 576 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.034 (285 hom., cov: 32)
  • Exomes 𝑓: 0.0035 (291 hom.)
• Consequence: TAS2R16 NM_016945.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP7: Synonymous conserved (PhyloP=-0.687 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R16	NM_016945.3	c.460T>C	p.Leu154Leu	synonymous_variant	1/1	ENST00000249284.3	NP_058641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R16	ENST00000249284.3	c.460T>C	p.Leu154Leu	synonymous_variant	1/1	6	NM_016945.3	ENSP00000249284.2

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5139 AN: 152024 Hom.: 284 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.0224

GnomAD3 exomes AF: 0.00880 AC: 2205 AN: 250526 Hom.: 134 AF XY: 0.00638 AC XY: 864 AN XY: 135366

Gnomad AFR exome AF: 0.120

Gnomad AMR exome AF: 0.00530

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000196

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000372

Gnomad OTH exome AF: 0.00442

GnomAD4 exome AF: 0.00351 AC: 5131 AN: 1461668 Hom.: 291 Cov.: 33 AF XY: 0.00298 AC XY: 2170 AN XY: 727128

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.00619

Gnomad4 ASJ exome AF: 0.0000766

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000243

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000153

Gnomad4 OTH exome AF: 0.00793

GnomAD4 genome AF: 0.0338 AC: 5150 AN: 152142 Hom.: 285 Cov.: 32 AF XY: 0.0321 AC XY: 2384 AN XY: 74382

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000368

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0181 Hom.: 70

Bravo AF: 0.0391

Asia WGS AF: 0.0110 AC: 37 AN: 3478

EpiCase AF: 0.000654

EpiControl AF: 0.000593

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2233989; hg19: chr7-122635229;