rs4726600

Positions:

• chr7-143184447-G-A
• chr7-143184447-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 7-143184447-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,581,058 control chromosomes in the GnomAD database, including 43,166 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 0.17 (2998 hom., cov: 32)
  • Exomes 𝑓: 0.22 (40168 hom.)
• Consequence: TAS2R39 NM_176881.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

TAS2R39 (HGNC:18886): (taste 2 receptor member 39) The protein encoded by this gene is a bitter taste receptor that detects green tea catechins, soy isoflavones, and theaflavins. The encoded protein is gustducin-linked and may activate alpha gustducin. This gene is intronless. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R39	NM_176881.2			downstream_gene_variant		ENST00000446620.1	NP_795362.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R39	ENST00000446620.1			downstream_gene_variant			NM_176881.2	ENSP00000405095	P1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25576 AN: 151766 Hom.: 2997 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.178

GnomAD3 exomes AF: 0.173 AC: 36088 AN: 208340 Hom.: 4012 AF XY: 0.175 AC XY: 19613 AN XY: 112132

Gnomad AFR exome AF: 0.0448

Gnomad AMR exome AF: 0.109

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.0140

Gnomad SAS exome AF: 0.103

Gnomad FIN exome AF: 0.280

Gnomad NFE exome AF: 0.238

Gnomad OTH exome AF: 0.190

GnomAD4 exome AF: 0.220 AC: 314028 AN: 1429174 Hom.: 40168 Cov.: 33 AF XY: 0.217 AC XY: 153756 AN XY: 708534

Gnomad4 AFR exome AF: 0.0424

Gnomad4 AMR exome AF: 0.112

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.0114

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.278

Gnomad4 NFE exome AF: 0.245

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.168 AC: 25571 AN: 151884 Hom.: 2998 Cov.: 32 AF XY: 0.167 AC XY: 12419 AN XY: 74248

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.176

Alfa AF: 0.218 Hom.: 5814

Bravo AF: 0.154

Asia WGS AF: 0.0470 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4726600; hg19: chr7-142881540;