rs3211834

chr7-80650801-A-Cchr7-80650801-A-Gchr7-80650801-A-T

Variant summary

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

The NM_001001548.3(CD36):c.120+3941A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,672 control chromosomes in the GnomAD database, including 32,626 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 0.65 (32626 hom., cov: 30)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.120+3941A>C		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.120+3941A>C		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99090 AN: 151552 Hom.: 32602 Cov.: 30

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.654 AC: 99170 AN: 151672 Hom.: 32626 Cov.: 30 AF XY: 0.651 AC XY: 48250 AN XY: 74070

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.650

Alfa AF: 0.606 Hom.: 11135

Bravo AF: 0.663

Asia WGS AF: 0.595 AC: 2064 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.68
Dann	Benign	0.83

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: rs3211834; hg19: chr7-80280117;