rs1358337

Variant names:

• chr7-80659069-G-A
• rs1358337
• NM_001001548.3:c.282-1994G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001548.3(CD36):​c.282-1994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,918 control chromosomes in the GnomAD database, including 17,699 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 0.48 (17699 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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.282-1994G>A		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_000072.3		c.282-1994G>A		intron	N/A	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.282-1994G>A		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.282-1994G>A		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000309881.11	TSL:1	c.282-1994G>A		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000394788.7	TSL:1	c.282-1994G>A		intron	N/A	ENSP00000378268.3	P16671-1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72205 AN: 151802 Hom.: 17676 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.476 AC: 72279 AN: 151918 Hom.: 17699 Cov.: 32 AF XY: 0.481 AC XY: 35692 AN XY: 74214

African (AFR) AF: 0.543 AC: 22488 AN: 41406

American (AMR) AF: 0.454 AC: 6928 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3182 AN: 5142

South Asian (SAS) AF: 0.695 AC: 3354 AN: 4824

European-Finnish (FIN) AF: 0.442 AC: 4668 AN: 10550

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28757 AN: 67956

Other (OTH) AF: 0.461 AC: 971 AN: 2108

Alfa AF: 0.450 Hom.: 3042

Bravo AF: 0.472

Asia WGS AF: 0.677 AC: 2349 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.056
DANN	Benign	0.12
PhyloP100		-1.4
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: rs1358337; hg19: chr7-80288385;