chr1-18843474-A-T

Variant names:

• chr1-18843474-A-T
• rs12567264
• NM_152232.6:c.1468-1622T>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.1468-1622T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,028 control chromosomes in the GnomAD database, including 7,736 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 (7736 hom., cov: 32)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1468-1622T>A		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.1468-1622T>A		intron_variant	Intron 4 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47302 AN: 151910 Hom.: 7736 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.311 AC: 47325 AN: 152028 Hom.: 7736 Cov.: 32 AF XY: 0.308 AC XY: 22868 AN XY: 74312

African (AFR) AF: 0.240 AC: 9942 AN: 41446

American (AMR) AF: 0.279 AC: 4264 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3472

East Asian (EAS) AF: 0.447 AC: 2307 AN: 5166

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4820

European-Finnish (FIN) AF: 0.312 AC: 3289 AN: 10548

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24259 AN: 67986

Other (OTH) AF: 0.302 AC: 638 AN: 2112

Alfa AF: 0.322 Hom.: 996

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	-0.92
CADD	Benign	6.3
DANN	Benign	0.72
PhyloP100		0.29
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: rs12567264; hg19: chr1-19169968;