rs3211913

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

CD36 Gene-Disease associations (from GenCC):

• platelet-type bleeding disorder 10

  Inheritance: AR Classification: STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001548.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.701+791A>G		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_000072.3		c.701+791A>G		intron	N/A	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.701+791A>G		intron	N/A	NP_001001547.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.701+791A>G		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000309881.11	TSL:1	c.701+791A>G		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000394788.7	TSL:1	c.701+791A>G		intron	N/A	ENSP00000378268.3	P16671-1

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

African (AFR) AF: 0.355 AC: 14671 AN: 41360

American (AMR) AF: 0.0896 AC: 1365 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3464

East Asian (EAS) AF: 0.0881 AC: 455 AN: 5162

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4828

European-Finnish (FIN) AF: 0.0185 AC: 196 AN: 10580

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1618 AN: 67966

Other (OTH) AF: 0.0907 AC: 191 AN: 2106

Alfa AF: 0.100 Hom.: 307

Bravo AF: 0.141

Asia WGS AF: 0.0740 AC: 256 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.80
DANN	Benign	0.77
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3211913; hg19: chr7-80294604;