rs3211830

chr7-80650402-C-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+3542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 151,812 control chromosomes in the GnomAD database, including 1,057 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 0.10 (1057 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.120+3542C>T		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.120+3542C>T		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15170 AN: 151696 Hom.: 1060 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.0695

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.0449

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.0999 AC: 15171 AN: 151812 Hom.: 1057 Cov.: 32 AF XY: 0.102 AC XY: 7582 AN XY: 74218

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.0695

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0985

Alfa AF: 0.0748 Hom.: 489

Bravo AF: 0.0973

Asia WGS AF: 0.280 AC: 970 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.1
Dann	Benign	0.53

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: rs3211830; hg19: chr7-80279718;