rs12408808

Positions:

• chr1-18844452-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1468-2600T>C		intron_variant		ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1468-2600T>C		intron_variant		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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.659

Alfa AF: 0.715 Hom.: 36612

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

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: rs12408808; hg19: chr1-19170946;