rs7784820

Variant names:

• chr7-80420717-A-G
• rs7784820
• ENST00000435819.5:c.-478+50936A>G

Variant summary

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

The ENST00000435819.5(CD36):​c.-478+50936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,180 control chromosomes in the GnomAD database, including 2,621 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 0.15 (2621 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

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]

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

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 = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435819.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000435819.5	TSL:2	c.-478+50936A>G		intron	N/A	ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23332 AN: 152062 Hom.: 2607 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0925

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0817

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.154 AC: 23397 AN: 152180 Hom.: 2621 Cov.: 32 AF XY: 0.150 AC XY: 11185 AN XY: 74404

African (AFR) AF: 0.316 AC: 13126 AN: 41482

American (AMR) AF: 0.108 AC: 1647 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0925 AC: 321 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5178

South Asian (SAS) AF: 0.143 AC: 692 AN: 4824

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0817 AC: 5553 AN: 68004

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.120 Hom.: 200

Bravo AF: 0.163

Asia WGS AF: 0.197 AC: 683 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.46
PhyloP100		-1.1
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: rs7784820; hg19: chr7-80050033;