1-18852610-G-T

Variant names:

• chr1-18852610-G-T
• rs4920564
• NM_152232.6:c.1257+1603C>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.1257+1603C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,026 control chromosomes in the GnomAD database, including 40,326 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 0.72 (40326 hom., cov: 31)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1257+1603C>A		intron_variant	Intron 3 of 5	ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1257+1603C>A		intron_variant	Intron 3 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109209 AN: 151908 Hom.: 40286 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.719 AC: 109301 AN: 152026 Hom.: 40326 Cov.: 31 AF XY: 0.726 AC XY: 53957 AN XY: 74296

African (AFR) AF: 0.853 AC: 35356 AN: 41472

American (AMR) AF: 0.729 AC: 11147 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2148 AN: 3466

East Asian (EAS) AF: 0.961 AC: 4968 AN: 5170

South Asian (SAS) AF: 0.780 AC: 3753 AN: 4810

European-Finnish (FIN) AF: 0.712 AC: 7523 AN: 10562

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42202 AN: 67948

Other (OTH) AF: 0.722 AC: 1525 AN: 2112

Alfa AF: 0.669 Hom.: 58248

Bravo AF: 0.723

Asia WGS AF: 0.863 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.078
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: rs4920564; hg19: chr1-19179104;