1-18840877-G-T

Variant names:

• chr1-18840877-G-T
• rs3935570
• NM_152232.6:c.1592-350C>A

Variant summary

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

The NM_152232.6(TAS1R2):​c.1592-350C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,112 control chromosomes in the GnomAD database, including 5,604 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 0.26 (5604 hom., cov: 32)
• Consequence: TAS1R2 NM_152232.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R2	NM_152232.6	c.1592-350C>A		intron_variant	Intron 5 of 5	ENST00000375371.4	NP_689418.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R2	ENST00000375371.4	c.1592-350C>A		intron_variant	Intron 5 of 5	2	NM_152232.6	ENSP00000364520.3

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40180 AN: 151994 Hom.: 5587 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.265 AC: 40238 AN: 152112 Hom.: 5604 Cov.: 32 AF XY: 0.260 AC XY: 19315 AN XY: 74350

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.251

Alfa AF: 0.261 Hom.: 7474

Bravo AF: 0.261

Asia WGS AF: 0.212 AC: 734 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	0.084
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3935570; hg19: chr1-19167371;