rs6975345

Variant names:

• chr7-80494683-T-C
• rs6975345
• NM_001102386.3:c.119-36A>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 11 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

LOC107986812 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102386.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAT3	NM_001102386.3	MANE Select	c.119-36A>G		intron	N/A	NP_001095856.1	A8MTJ3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAT3	ENST00000398291.4	TSL:1 MANE Select	c.119-36A>G		intron	N/A	ENSP00000381339.3	A8MTJ3
	CD36	ENST00000435819.5	TSL:2	c.-261+6902T>C		intron	N/A	ENSP00000399421.1	P16671-1
	CD36	ENST00000956914.1		c.-261+6902T>C		intron	N/A	ENSP00000626973.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41382 AN: 152020 Hom.: 10253 Cov.: 32

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

GnomAD2 exomes AF: 0.151 AC: 24619 AN: 163108 AF XY: 0.145

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 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.: 14 AF XY: 0.132 AC XY: 71681 AN XY: 541684

African (AFR) AF: 0.689 AC: 17326 AN: 25146

American (AMR) AF: 0.104 AC: 3636 AN: 34996

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 2648 AN: 22910

East Asian (EAS) AF: 0.128 AC: 4520 AN: 35206

South Asian (SAS) AF: 0.119 AC: 8454 AN: 70978

European-Finnish (FIN) AF: 0.0882 AC: 4399 AN: 49848

Middle Eastern (MID) AF: 0.176 AC: 873 AN: 4958

European-Non Finnish (NFE) AF: 0.122 AC: 94373 AN: 776346

Other (OTH) AF: 0.160 AC: 7477 AN: 46862

GnomAD4 genome AF: 0.273 AC: 41466 AN: 152138 Hom.: 10283 Cov.: 32 AF XY: 0.265 AC XY: 19695 AN XY: 74370

African (AFR) AF: 0.669 AC: 27717 AN: 41438

American (AMR) AF: 0.144 AC: 2193 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.147 AC: 760 AN: 5184

South Asian (SAS) AF: 0.130 AC: 629 AN: 4828

European-Finnish (FIN) AF: 0.0864 AC: 917 AN: 10618

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.121 AC: 8216 AN: 68008

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.165 Hom.: 14141

Bravo AF: 0.294

Asia WGS AF: 0.162 AC: 564 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.64
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6975345; hg19: chr7-80123999; COSMIC: COSV68068852;