rs704871

Positions:

• chr7-80436361-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-477-50106T>C		intron_variant		2		ENSP00000399421	P1

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.722

Alfa AF: 0.756 Hom.: 87767

Bravo AF: 0.726

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.41

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: rs704871; hg19: chr7-80065677;