rs6962693

Positions:

• chr7-80504716-T-G

Variant summary

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

The NM_001102386.3(GNAT3):​c.118+7093A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,018 control chromosomes in the GnomAD database, including 10,355 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 0.36 (10355 hom., cov: 32)
• Consequence: GNAT3 NM_001102386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

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]

LOC107986812 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAT3	NM_001102386.3	c.118+7093A>C		intron_variant		ENST00000398291.4	NP_001095856.1
LOC107986812	XR_001745252.2	n.218-8329T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4	c.118+7093A>C		intron_variant		1	NM_001102386.3	ENSP00000381339	P1
CD36	ENST00000435819.5	c.-261+16935T>G		intron_variant		2		ENSP00000399421	P1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54445 AN: 151900 Hom.: 10353 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.358 AC: 54452 AN: 152018 Hom.: 10355 Cov.: 32 AF XY: 0.356 AC XY: 26448 AN XY: 74296

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.343

Alfa AF: 0.345 Hom.: 5265

Bravo AF: 0.360

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs6962693; hg19: chr7-80134032;