rs12137730

Variant names:

• chr1-18843094-A-C
• rs12137730
• NM_152232.6:c.1468-1242T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.96).
• 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 rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1468-1242T>G		intron_variant	Intron 4 of 5	ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1468-1242T>G		intron_variant	Intron 4 of 5	2	NM_152232.6	ENSP00000364520.3

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

African (AFR) AF: 0.192 AC: 7970 AN: 41502

American (AMR) AF: 0.345 AC: 5278 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3470

East Asian (EAS) AF: 0.105 AC: 545 AN: 5182

South Asian (SAS) AF: 0.263 AC: 1268 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3932 AN: 10570

Middle Eastern (MID) AF: 0.288 AC: 83 AN: 288

European-Non Finnish (NFE) AF: 0.367 AC: 24961 AN: 67938

Other (OTH) AF: 0.309 AC: 651 AN: 2106

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
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12137730; hg19: chr1-19169588;