rs4920566

chr1-18853330-A-G

Variant summary

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

The NM_152232.6(TAS1R2):c.1257+883T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,078 control chromosomes in the GnomAD database, including 20,791 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 0.50 (20791 hom., cov: 33)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

Genes affected

TAS1R2 (HGNC:14905): (taste 1 receptor member 2) Contributes to sweet taste receptor activity. Involved in detection of chemical stimulus involved in sensory perception of sweet taste and positive regulation of cytokinesis. Part of sweet taste receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R2	NM_152232.6	c.1257+883T>C		intron_variant		ENST00000375371.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1257+883T>C		intron_variant		2	NM_152232.6	P1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76248 AN: 151958 Hom.: 20764 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.468

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.502 AC: 76328 AN: 152078 Hom.: 20791 Cov.: 33 AF XY: 0.505 AC XY: 37541 AN XY: 74342

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.471

Alfa AF: 0.439 Hom.: 9470

Bravo AF: 0.503

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.59
Dann	Benign	0.43

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: rs4920566; hg19: chr1-19179824;