NM_152232.6:c.1258-864G>A

Variant names:

• chr1-18850414-C-T
• rs4076838
• NM_152232.6:c.1258-864G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152232.6(TAS1R2):​c.1258-864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,214 control chromosomes in the GnomAD database, including 20,168 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 (20168 hom., cov: 34)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.96
• Publications: 0 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 = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1258-864G>A		intron_variant	Intron 3 of 5	ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1258-864G>A		intron_variant	Intron 3 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75525 AN: 152096 Hom.: 20150 Cov.: 34

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.497 AC: 75580 AN: 152214 Hom.: 20168 Cov.: 34 AF XY: 0.492 AC XY: 36618 AN XY: 74416

African (AFR) AF: 0.334 AC: 13865 AN: 41524

American (AMR) AF: 0.499 AC: 7638 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3472

East Asian (EAS) AF: 0.187 AC: 966 AN: 5176

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4820

European-Finnish (FIN) AF: 0.540 AC: 5726 AN: 10600

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41062 AN: 68004

Other (OTH) AF: 0.500 AC: 1058 AN: 2114

Alfa AF: 0.570 Hom.: 30544

Bravo AF: 0.483

Asia WGS AF: 0.322 AC: 1122 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	0.0050
DANN	Benign	0.40
PhyloP100		-5.0
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: rs4076838; hg19: chr1-19176908;