rs4908932

chr1-6579787-G-T

Variant summary

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

The 1-6579787-G-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 705,564 control chromosomes in the GnomAD database, including 11,330 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 (2510 hom., cov: 33)
  • Exomes 𝑓: 0.17 (8820 hom.)
• Consequence: TAS1R1 NM_138697.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

TAS1R1 (HGNC:14448): (taste 1 receptor member 1) The protein encoded by this gene is a G protein-coupled receptor and is a component of the heterodimeric amino acid taste receptor T1R1+3. The T1R1+3 receptor responds to L-amino acids but not to D-enantiomers or other compounds. Most amino acids that are perceived as sweet activate T1R1+3, and this activation is strictly dependent on an intact T1R1+3 heterodimer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R1	NM_138697.4			downstream_gene_variant		ENST00000333172.11
TAS1R1	NM_177540.3			downstream_gene_variant
TAS1R1	XM_011542203.2			downstream_gene_variant
TAS1R1	XM_011542206.3			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R1	ENST00000333172.11			downstream_gene_variant		1	NM_138697.4	P1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25329 AN: 152126 Hom.: 2505 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.167 AC: 92180 AN: 553320 Hom.: 8820 Cov.: 7 AF XY: 0.164 AC XY: 46731 AN XY: 284358

Gnomad4 AFR exome AF: 0.109

Gnomad4 AMR exome AF: 0.340

Gnomad4 ASJ exome AF: 0.174

Gnomad4 EAS exome AF: 0.000393

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.207

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.166 AC: 25339 AN: 152244 Hom.: 2510 Cov.: 33 AF XY: 0.168 AC XY: 12475 AN XY: 74446

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0971

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.167

Alfa AF: 0.174 Hom.: 3067

Bravo AF: 0.172

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.2
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4908932; hg19: chr1-6639847;