rs2065668

Positions:

• chr7-80591292-C-T

Variant summary

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

The ENST00000435819.5(CD36):​c.-184+45025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,844 control chromosomes in the GnomAD database, including 8,873 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 0.34 (8873 hom., cov: 31)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80591292C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+45025C>T		intron_variant		2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51574 AN: 151724 Hom.: 8865 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51612 AN: 151844 Hom.: 8873 Cov.: 31 AF XY: 0.342 AC XY: 25362 AN XY: 74216

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.341

Alfa AF: 0.353 Hom.: 19520

Bravo AF: 0.332

Asia WGS AF: 0.395 AC: 1370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.32

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: rs2065668; hg19: chr7-80220608;