rs6467212

Variant names:

• chr7-80488688-A-G
• rs6467212
• NM_001102386.3:c.162-12T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-80488688-A-G
• chr7-80488688-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001102386.3(GNAT3):​c.162-12T>C 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 1,551,694 control chromosomes in the GnomAD database, including 9,282 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 0.12 (1218 hom., cov: 32)
  • Exomes 𝑓: 0.10 (8064 hom.)
• Consequence: GNAT3 NM_001102386.3 intron
• Scores: Splicing: ADA: 0.003910
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88
• Publications: 6 publications found

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]

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

LOC107986812 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAT3	NM_001102386.3	c.162-12T>C		intron_variant	Intron 2 of 7	ENST00000398291.4	NP_001095856.1
LOC107986812	XR_001745252.2	n.217+907A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAT3	ENST00000398291.4	c.162-12T>C		intron_variant	Intron 2 of 7	1	NM_001102386.3	ENSP00000381339.3
CD36	ENST00000435819.5	c.-261+907A>G		intron_variant	Intron 3 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17891 AN: 152026 Hom.: 1210 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.109

GnomAD2 exomes AF: 0.0929 AC: 16464 AN: 177230 AF XY: 0.0920

Gnomad AFR exome AF: 0.197

Gnomad AMR exome AF: 0.0542

Gnomad ASJ exome AF: 0.0552

Gnomad EAS exome AF: 0.107

Gnomad FIN exome AF: 0.0710

Gnomad NFE exome AF: 0.106

Gnomad OTH exome AF: 0.0890

GnomAD4 exome AF: 0.103 AC: 143815 AN: 1399550 Hom.: 8064 Cov.: 26 AF XY: 0.102 AC XY: 70348 AN XY: 691508

African (AFR) AF: 0.199 AC: 6420 AN: 32322

American (AMR) AF: 0.0566 AC: 2111 AN: 37276

Ashkenazi Jewish (ASJ) AF: 0.0506 AC: 1266 AN: 25002

East Asian (EAS) AF: 0.0994 AC: 3740 AN: 37618

South Asian (SAS) AF: 0.0715 AC: 5682 AN: 79522

European-Finnish (FIN) AF: 0.0725 AC: 3601 AN: 49638

Middle Eastern (MID) AF: 0.103 AC: 583 AN: 5638

European-Non Finnish (NFE) AF: 0.107 AC: 114691 AN: 1074568

Other (OTH) AF: 0.0987 AC: 5721 AN: 57966

GnomAD4 genome AF: 0.118 AC: 17919 AN: 152144 Hom.: 1218 Cov.: 32 AF XY: 0.114 AC XY: 8498 AN XY: 74370

African (AFR) AF: 0.186 AC: 7736 AN: 41506

American (AMR) AF: 0.0676 AC: 1031 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3468

East Asian (EAS) AF: 0.107 AC: 554 AN: 5174

South Asian (SAS) AF: 0.0700 AC: 338 AN: 4826

European-Finnish (FIN) AF: 0.0712 AC: 755 AN: 10606

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 7024 AN: 67992

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.0926 Hom.: 363

Bravo AF: 0.121

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		2.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0039
dbscSNV1_RF	Benign	0.14
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6467212; hg19: chr7-80118004; COSMIC: COSV68068903;