rs12137730

Positions:

• chr1-18843094-A-C

Variant summary

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

The NM_152232.6(TAS1R2):​c.1468-1242T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,066 control chromosomes in the GnomAD database, including 7,702 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 (7702 hom., cov: 33)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1468-1242T>G		intron_variant		ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1468-1242T>G		intron_variant		2	NM_152232.6	ENSP00000364520	P1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46389 AN: 151948 Hom.: 7699 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.305 AC: 46399 AN: 152066 Hom.: 7702 Cov.: 33 AF XY: 0.306 AC XY: 22726 AN XY: 74364

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.309

Alfa AF: 0.341 Hom.: 1277

Bravo AF: 0.298

Asia WGS AF: 0.172 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	14
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs12137730; hg19: chr1-19169588;