rs3211913

Variant names:

• chr7-80665288-A-G
• rs3211913
• NM_001001548.3:c.701+791A>G

Variant summary

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

The NM_001001548.3(CD36):​c.701+791A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,914 control chromosomes in the GnomAD database, including 2,803 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 0.12 (2803 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.701+791A>G		intron_variant	Intron 7 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.701+791A>G		intron_variant	Intron 7 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18724 AN: 151798 Hom.: 2783 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.124 AC: 18789 AN: 151914 Hom.: 2803 Cov.: 32 AF XY: 0.121 AC XY: 8977 AN XY: 74288

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.0896

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0185

Gnomad4 NFE AF: 0.0238

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0906 Hom.: 254

Bravo AF: 0.141

Asia WGS AF: 0.0740 AC: 256 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.77

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: rs3211913; hg19: chr7-80294604;