1-18847120-G-T

Variant names:

• chr1-18847120-G-T
• rs7513755
• NM_152232.6:c.1467+2221C>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.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
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152232.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R2	NM_152232.6	MANE Select	c.1467+2221C>A		intron	N/A	NP_689418.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R2	ENST00000375371.4	TSL:2 MANE Select	c.1467+2221C>A		intron	N/A	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

African (AFR) AF: 0.744 AC: 30827 AN: 41456

American (AMR) AF: 0.868 AC: 13268 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2781 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4569 AN: 5168

South Asian (SAS) AF: 0.826 AC: 3982 AN: 4820

European-Finnish (FIN) AF: 0.918 AC: 9744 AN: 10610

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59455 AN: 68008

Other (OTH) AF: 0.856 AC: 1810 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.70
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: rs7513755; hg19: chr1-19173614;