Variant rs2270009 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_016943.2(TAS2R3):c.807C>T(p.Gly269Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 1,613,878 control chromosomes in the GnomAD database, including 185,168 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 0.42 ( 14387 hom., cov: 33)

Exomes 𝑓: 0.48 ( 170781 hom. )

Consequence

TAS2R3
NM_016943.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Variant links:

Genes affected

TAS2R3 (HGNC:14910): (taste 2 receptor member 3) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily and that are specifically expressed by taste receptor cells of the tongue and palate epithelia. These apparently intronless taste receptor genes encode a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes in chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

TAS2R3 links:

SSBP1 (HGNC:11317): (single stranded DNA binding protein 1) SSBP1 is a housekeeping gene involved in mitochondrial biogenesis (Tiranti et al., 1995 [PubMed 7789991]). It is also a subunit of a single-stranded DNA (ssDNA)-binding complex involved in the maintenance of genome stability (Huang et al., 2009) [PubMed 19683501].[supplied by OMIM, Feb 2010]

SSBP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=-0.306 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R3	NM_016943.2 linkuse as main transcript	c.807C>T	p.Gly269Gly	synonymous_variant	1/1	ENST00000247879.2	NP_058639.1	Q9NYW6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R3	ENST00000247879.2 linkuse as main transcript	c.807C>T	p.Gly269Gly	synonymous_variant	1/1	6	NM_016943.2	ENSP00000247879.2		Q9NYW6
SSBP1	ENST00000465582.5 linkuse as main transcript	c.*30+14581C>T		intron_variant		5		ENSP00000420485.1		Q04837

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63736

AN:

151914

Hom.:

14380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.687

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.449

GnomAD3 exomes

AF:

0.476

AC:

119743

AN:

251406

Hom.:

29713

AF XY:

0.480

AC XY:

65228

AN XY:

135864

show subpopulations

Gnomad AFR exome

AF:

0.221

Gnomad AMR exome

AF:

0.489

Gnomad ASJ exome

AF:

0.456

Gnomad EAS exome

AF:

0.691

Gnomad SAS exome

AF:

0.450

Gnomad FIN exome

AF:

0.460

Gnomad NFE exome

AF:

0.485

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.481

AC:

702447

AN:

1461844

Hom.:

170781

Cov.:

AF XY:

0.482

AC XY:

350249

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.494

Gnomad4 ASJ exome

AF:

0.453

Gnomad4 EAS exome

AF:

0.674

Gnomad4 SAS exome

AF:

0.453

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.419

AC:

63772

AN:

152034

Hom.:

14387

Cov.:

AF XY:

0.422

AC XY:

31377

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.488

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.686

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.461

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.474

Hom.:

24268

Bravo

AF:

0.416

Asia WGS

AF:

0.552

AC:

1917

AN:

3478

EpiCase

AF:

0.495

EpiControl

AF:

0.495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

3.9

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over