rs3211868

Positions:

• chr7-80657706-T-C

Variant summary

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

The NM_001001548.3(CD36):​c.281+1006T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,080 control chromosomes in the GnomAD database, including 2,016 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 0.13 (2016 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001548.3	c.281+1006T>C		intron_variant		ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.281+1006T>C		intron_variant		5	NM_001001548.3	ENSP00000415743	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20413 AN: 151962 Hom.: 2009 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.134 AC: 20445 AN: 152080 Hom.: 2016 Cov.: 32 AF XY: 0.137 AC XY: 10171 AN XY: 74328

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.125

Alfa AF: 0.112 Hom.: 183

Bravo AF: 0.139

Asia WGS AF: 0.342 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.63
DANN	Benign	0.46

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: rs3211868; hg19: chr7-80287022;