rs1548803

Positions:

• chr12-10806432-C-T

Variant summary

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

The NM_023918.3(TAS2R8):​c.549G>A​(p.Leu183=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 1,613,422 control chromosomes in the GnomAD database, including 279,485 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 0.51 (21791 hom., cov: 31)
  • Exomes 𝑓: 0.59 (257694 hom.)
• Consequence: TAS2R8 NM_023918.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

TAS2R8 (HGNC:14915): (taste 2 receptor member 8) 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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=0.052 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R8	NM_023918.3	c.549G>A	p.Leu183=	synonymous_variant	1/1	ENST00000240615.3	NP_076407.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R8	ENST00000240615.3	c.549G>A	p.Leu183=	synonymous_variant	1/1		NM_023918.3	ENSP00000240615	P1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76739 AN: 151778 Hom.: 21807 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.538

GnomAD3 exomes AF: 0.590 AC: 147696 AN: 250312 Hom.: 45094 AF XY: 0.598 AC XY: 80889 AN XY: 135290

Gnomad AFR exome AF: 0.220

Gnomad AMR exome AF: 0.572

Gnomad ASJ exome AF: 0.676

Gnomad EAS exome AF: 0.664

Gnomad SAS exome AF: 0.597

Gnomad FIN exome AF: 0.686

Gnomad NFE exome AF: 0.608

Gnomad OTH exome AF: 0.609

GnomAD4 exome AF: 0.590 AC: 862460 AN: 1461526 Hom.: 257694 Cov.: 64 AF XY: 0.592 AC XY: 430468 AN XY: 727052

Gnomad4 AFR exome AF: 0.221

Gnomad4 AMR exome AF: 0.573

Gnomad4 ASJ exome AF: 0.680

Gnomad4 EAS exome AF: 0.668

Gnomad4 SAS exome AF: 0.591

Gnomad4 FIN exome AF: 0.681

Gnomad4 NFE exome AF: 0.593

Gnomad4 OTH exome AF: 0.581

GnomAD4 genome AF: 0.505 AC: 76728 AN: 151896 Hom.: 21791 Cov.: 31 AF XY: 0.512 AC XY: 37976 AN XY: 74218

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.537

Alfa AF: 0.592 Hom.: 45121

Bravo AF: 0.484

Asia WGS AF: 0.591 AC: 2054 AN: 3478

EpiCase AF: 0.614

EpiControl AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs1548803; hg19: chr12-10959031; COSMIC: COSV53688247; COSMIC: COSV53688247;