Variant 7-80494683-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001102386.3(GNAT3):c.119-36A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,219,388 control chromosomes in the GnomAD database, including 24,585 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 0.27 ( 10283 hom., cov: 32)

Exomes 𝑓: 0.13 ( 14302 hom. )

Consequence

GNAT3
NM_001102386.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

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:

LOC107986812 (HGNC:):

LOC107986812 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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.119-36A>G		intron_variant		ENST00000398291.4	NP_001095856.1
LOC107986812	XR_001745252.2 linkuse as main transcript	n.217+6902T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4 linkuse as main transcript	c.119-36A>G		intron_variant		1	NM_001102386.3	ENSP00000381339	P1
CD36	ENST00000435819.5 linkuse as main transcript	c.-261+6902T>C		intron_variant		2		ENSP00000399421	P1	P16671-1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41382

AN:

152020

Hom.:

10253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.0864

Gnomad MID

AF:

0.182

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.223

GnomAD3 exomes

AF:

0.151

AC:

24619

AN:

163108

Hom.:

3384

AF XY:

0.145

AC XY:

12433

AN XY:

85938

show subpopulations

Gnomad AFR exome

AF:

0.688

Gnomad AMR exome

AF:

0.0958

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.148

Gnomad SAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.0863

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.133

GnomAD4 exome

AF:

0.135

AC:

143706

AN:

1067250

Hom.:

14302

Cov.:

AF XY:

0.132

AC XY:

71681

AN XY:

541684

show subpopulations

Gnomad4 AFR exome

AF:

0.689

Gnomad4 AMR exome

AF:

0.104

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.0882

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.160

GnomAD4 genome

AF:

0.273

AC:

41466

AN:

152138

Hom.:

10283

Cov.:

AF XY:

0.265

AC XY:

19695

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.121

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.0864

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.139

Hom.:

3605

Bravo

AF:

0.294

Asia WGS

AF:

0.162

AC:

564

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

DANN

Benign

0.64

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