1-18847120-G-T

Variant names:

• chr1-18847120-G-T
• rs7513755
• NM_152232.6:c.1467+2221C>A

Variant summary

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

The NM_152232.6(TAS1R2):​c.1467+2221C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,132 control chromosomes in the GnomAD database, including 53,674 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 0.84 (53674 hom., cov: 32)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1467+2221C>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.1467+2221C>A		intron_variant	Intron 4 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127328 AN: 152014 Hom.: 53642 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.838 AC: 127416 AN: 152132 Hom.: 53674 Cov.: 32 AF XY: 0.838 AC XY: 62325 AN XY: 74386

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.856

Alfa AF: 0.851 Hom.: 6846

Bravo AF: 0.830

Asia WGS AF: 0.813 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.53

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: rs7513755; hg19: chr1-19173614;