rs704871

Variant names:

• chr7-80436361-T-C
• rs704871
• ENST00000435819.5:c.-477-50106T>C

Variant summary

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

The ENST00000435819.5(CD36):​c.-477-50106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,064 control chromosomes in the GnomAD database, including 41,105 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 0.73 (41105 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 4 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000435819.5	TSL:2	c.-477-50106T>C		intron	N/A	ENSP00000399421.1	P16671-1
	CD36	ENST00000956914.1		c.-477-50106T>C		intron	N/A	ENSP00000626973.1
	CD36	ENST00000956916.1		c.-473-50106T>C		intron	N/A	ENSP00000626975.1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111406 AN: 151946 Hom.: 41077 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.733 AC: 111481 AN: 152064 Hom.: 41105 Cov.: 32 AF XY: 0.735 AC XY: 54650 AN XY: 74330

African (AFR) AF: 0.653 AC: 27052 AN: 41446

American (AMR) AF: 0.757 AC: 11559 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2401 AN: 3466

East Asian (EAS) AF: 0.713 AC: 3681 AN: 5162

South Asian (SAS) AF: 0.728 AC: 3515 AN: 4828

European-Finnish (FIN) AF: 0.816 AC: 8639 AN: 10590

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52215 AN: 67992

Other (OTH) AF: 0.722 AC: 1522 AN: 2108

Alfa AF: 0.751 Hom.: 178614

Bravo AF: 0.726

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.41
PhyloP100		-0.89
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: rs704871; hg19: chr7-80065677;