rs4920566

Variant names:

• chr1-18853330-A-G
• rs4920566
• NM_152232.6:c.1257+883T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152232.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R2	NM_152232.6	MANE Select	c.1257+883T>C		intron	N/A	NP_689418.2	Q8TE23

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R2	ENST00000375371.4	TSL:2 MANE Select	c.1257+883T>C		intron	N/A	ENSP00000364520.3	Q8TE23

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

African (AFR) AF: 0.727 AC: 30134 AN: 41464

American (AMR) AF: 0.383 AC: 5860 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3074 AN: 5174

South Asian (SAS) AF: 0.532 AC: 2564 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4856 AN: 10544

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26994 AN: 67994

Other (OTH) AF: 0.471 AC: 996 AN: 2114

Alfa AF: 0.444 Hom.: 33848

Bravo AF: 0.503

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.59
DANN	Benign	0.43
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4920566; hg19: chr1-19179824;