rs10216027

Positions:

• chr7-80501215-T-C
• chr7-80501215-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.119-6568A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,052 control chromosomes in the GnomAD database, including 869 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 0.10 (869 hom., cov: 32)
• Consequence: GNAT3 NM_001102386.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAT3	NM_001102386.3	c.119-6568A>G		intron_variant		ENST00000398291.4	NP_001095856.1
LOC107986812	XR_001745252.2	n.218-11830T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4	c.119-6568A>G		intron_variant		1	NM_001102386.3	ENSP00000381339	P1
CD36	ENST00000435819.5	c.-261+13434T>C		intron_variant		2		ENSP00000399421	P1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15751 AN: 151934 Hom.: 868 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.104 AC: 15757 AN: 152052 Hom.: 869 Cov.: 32 AF XY: 0.101 AC XY: 7485 AN XY: 74310

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0652

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0818 Hom.: 256

Bravo AF: 0.105

Asia WGS AF: 0.0910 AC: 312 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.80

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: rs10216027; hg19: chr7-80130531;