dbSNP rs2074674: GNAT3:p.Asp337Asp (chr7-80458725-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

platelet-type bleeding disorder 10
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

CD36 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GNAT3	NM_001102386.3 link	c.1011C>T	p.Asp337Asp	synonymous_variant	Exon 8 of 8	ENST00000398291.4	NP_001095856.1	A8MTJ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4 link	c.1011C>T	p.Asp337Asp	synonymous_variant	Exon 8 of 8	1	NM_001102386.3	ENSP00000381339.3		A8MTJ3
CD36	ENST00000435819.5 link	c.-477-27742G>A		intron_variant	Intron 1 of 16	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

GnomAD2 exomes

AF:

0.390

AC:

88991

AN:

228330

AF XY:

0.381

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 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

African (AFR)

AF:

0.407

AC:

13303

AN:

32652

American (AMR)

AF:

0.450

AC:

18890

AN:

41996

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

6115

AN:

25794

East Asian (EAS)

AF:

0.762

AC:

29888

AN:

39236

South Asian (SAS)

AF:

0.398

AC:

32892

AN:

82660

European-Finnish (FIN)

AF:

0.412

AC:

21705

AN:

52718

Middle Eastern (MID)

AF:

0.215

AC:

1232

AN:

5728

European-Non Finnish (NFE)

AF:

0.324

AC:

354204

AN:

1094460

Other (OTH)

AF:

0.350

AC:

20802

AN:

59420

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

13115

26230

39345

52460

65575

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11740

23480

35220

46960

58700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.383

AC:

58180

AN:

151958

Hom.:

11739

Cov.:

AF XY:

0.391

AC XY:

29039

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.416

AC:

17224

AN:

41430

American (AMR)

AF:

0.407

AC:

6210

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.240

AC:

831

AN:

3468

East Asian (EAS)

AF:

0.759

AC:

3920

AN:

5164

South Asian (SAS)

AF:

0.423

AC:

2037

AN:

4816

European-Finnish (FIN)

AF:

0.412

AC:

4342

AN:

10546

Middle Eastern (MID)

AF:

0.216

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.330

AC:

22435

AN:

67956

Other (OTH)

AF:

0.361

AC:

762

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1806

3612

5418

7224

9030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.337

Hom.:

35189

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

(source)

DANN

Benign

0.74

PhyloP100

0.80

Mutation Taster

=96/4

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over