rs7534618

chr1-18843584-T-G

Variant summary

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

The NM_152232.6(TAS1R2):c.1468-1732A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,108 control chromosomes in the GnomAD database, including 7,749 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 0.31 (7749 hom., cov: 33)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R2	NM_152232.6	c.1468-1732A>C		intron_variant		ENST00000375371.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1468-1732A>C		intron_variant		2	NM_152232.6	P1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47361 AN: 151990 Hom.: 7749 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47384 AN: 152108 Hom.: 7749 Cov.: 33 AF XY: 0.308 AC XY: 22905 AN XY: 74368

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.302

Alfa AF: 0.347 Hom.: 17808

Bravo AF: 0.307

Asia WGS AF: 0.349 AC: 1216 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	2.2
Dann	Benign	0.66

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: rs7534618; hg19: chr1-19170078;