Variant rs2074674 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001102386.3(GNAT3):c.1011C>T(p.Asp337Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,586,622 control chromosomes in the GnomAD database, including 104,598 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 0.38 ( 11739 hom., cov: 32)

Exomes 𝑓: 0.35 ( 92859 hom. )

Consequence

GNAT3
NM_001102386.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.801

Variant links:

Genes affected

GNAT3 (HGNC:22800): (G protein subunit alpha transducin 3) Sweet, bitter, and umami tastes are transmitted from taste receptors by a specific guanine nucleotide binding protein. The protein encoded by this gene is the alpha subunit of this heterotrimeric G protein, which is found not only in the oral epithelium but also in gut tissues. Variations in this gene have been linked to metabolic syndrome. [provided by RefSeq, Dec 2015]

GNAT3 links:

CD36 (HGNC:1663): (CD36 molecule (CD36 blood group)) The protein encoded by this gene is the fourth major glycoprotein of the platelet surface and serves as a receptor for thrombospondin in platelets and various cell lines. Since thrombospondins are widely distributed proteins involved in a variety of adhesive processes, this protein may have important functions as a cell adhesion molecule. It binds to collagen, thrombospondin, anionic phospholipids and oxidized LDL. It directly mediates cytoadherence of Plasmodium falciparum parasitized erythrocytes and it binds long chain fatty acids and may function in the transport and/or as a regulator of fatty acid transport. Mutations in this gene cause platelet glycoprotein deficiency. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2014]

CD36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP7

Synonymous conserved (PhyloP=0.801 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAT3	NM_001102386.3 linkuse as main transcript	c.1011C>T	p.Asp337Asp	synonymous_variant	8/8	ENST00000398291.4	NP_001095856.1	A8MTJ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4 linkuse as main transcript	c.1011C>T	p.Asp337Asp	synonymous_variant	8/8	1	NM_001102386.3	ENSP00000381339.3		A8MTJ3
CD36	ENST00000435819.5 linkuse as main transcript	c.-477-27742G>A		intron_variant		2		ENSP00000399421.1		P16671-1

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58133

AN:

151840

Hom.:

11739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.407

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.759

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.226

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.365

GnomAD3 exomes

AF:

0.390

AC:

88991

AN:

228330

Hom.:

19182

AF XY:

0.381

AC XY:

46933

AN XY:

123188

show subpopulations

Gnomad AFR exome

AF:

0.419

Gnomad AMR exome

AF:

0.462

Gnomad ASJ exome

AF:

0.235

Gnomad EAS exome

AF:

0.763

Gnomad SAS exome

AF:

0.393

Gnomad FIN exome

AF:

0.410

Gnomad NFE exome

AF:

0.317

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.348

AC:

499031

AN:

1434664

Hom.:

92859

Cov.:

AF XY:

0.347

AC XY:

247554

AN XY:

713104

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.450

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.762

Gnomad4 SAS exome

AF:

0.398

Gnomad4 FIN exome

AF:

0.412

Gnomad4 NFE exome

AF:

0.324

Gnomad4 OTH exome

AF:

0.350

GnomAD4 genome

AF:

0.383

AC:

58180

AN:

151958

Hom.:

11739

Cov.:

AF XY:

0.391

AC XY:

29039

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.759

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.412

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.361

Alfa

AF:

0.323

Hom.:

15690

Bravo

AF:

0.384

Asia WGS

AF:

0.537

AC:

1867

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.74

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

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