rs12408808

Variant names:

• chr1-18844452-A-G
• rs12408808
• NM_152232.6:c.1468-2600T>C

Variant summary

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

The NM_152232.6(TAS1R2):​c.1468-2600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,106 control chromosomes in the GnomAD database, including 33,885 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 0.66 (33885 hom., cov: 32)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1468-2600T>C		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.1468-2600T>C		intron_variant	Intron 4 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100678 AN: 151986 Hom.: 33874 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.662 AC: 100717 AN: 152106 Hom.: 33885 Cov.: 32 AF XY: 0.657 AC XY: 48859 AN XY: 74334

African (AFR) AF: 0.566 AC: 23465 AN: 41470

American (AMR) AF: 0.657 AC: 10051 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2865 AN: 5176

South Asian (SAS) AF: 0.558 AC: 2692 AN: 4822

European-Finnish (FIN) AF: 0.691 AC: 7303 AN: 10566

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49790 AN: 67994

Other (OTH) AF: 0.659 AC: 1391 AN: 2112

Alfa AF: 0.707 Hom.: 47483

Bravo AF: 0.656

Asia WGS AF: 0.538 AC: 1872 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	5.9
DANN	Benign	0.76
PhyloP100		0.0010
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: rs12408808; hg19: chr1-19170946;