rs3211842

Positions:

• chr7-80653320-G-A
• chr7-80653320-G-C

Variant summary

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

The NM_001001548.3(CD36):​c.121-3220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,062 control chromosomes in the GnomAD database, including 13,671 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 0.42 (13671 hom., cov: 33)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.121-3220G>A		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.121-3220G>A		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63581 AN: 151944 Hom.: 13666 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.418 AC: 63612 AN: 152062 Hom.: 13671 Cov.: 33 AF XY: 0.423 AC XY: 31426 AN XY: 74320

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.418

Alfa AF: 0.408 Hom.: 1848

Bravo AF: 0.403

Asia WGS AF: 0.617 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.47

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: rs3211842; hg19: chr7-80282636;