7-80589645-C-T

Position:

• chr7-80589645-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+43378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,840 control chromosomes in the GnomAD database, including 16,640 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 0.46 (16640 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80589645C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+43378C>T		intron_variant		2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69938 AN: 151724 Hom.: 16623 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.461 AC: 69991 AN: 151840 Hom.: 16640 Cov.: 32 AF XY: 0.466 AC XY: 34558 AN XY: 74218

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.448

Alfa AF: 0.444 Hom.: 7267

Bravo AF: 0.454

Asia WGS AF: 0.686 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.71

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: rs6961069; hg19: chr7-80218961;