rs10499858

Variant names:

• chr7-80606530-A-G
• rs10499858
• ENST00000309881.11:c.-184+4151A>G

Variant summary

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

The NM_001001547.3(CD36):​c.-184+4151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,170 control chromosomes in the GnomAD database, including 1,486 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 (1486 hom., cov: 32)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 6 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: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

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 (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001547.3		c.-184+4151A>G		intron	N/A	NP_001001547.1
	CD36	NM_001371074.1		c.-180+4151A>G		intron	N/A	NP_001358003.1
	CD36	NM_001371075.1		c.-184+4151A>G		intron	N/A	NP_001358004.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+4151A>G		intron	N/A	ENSP00000308165.7
	CD36	ENST00000435819.5	TSL:2	c.-183-39558A>G		intron	N/A	ENSP00000399421.1
	CD36	ENST00000534394.5	TSL:2	c.-109+4151A>G		intron	N/A	ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17690 AN: 152050 Hom.: 1484 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0638

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.116 AC: 17708 AN: 152170 Hom.: 1486 Cov.: 32 AF XY: 0.119 AC XY: 8854 AN XY: 74410

African (AFR) AF: 0.183 AC: 7579 AN: 41470

American (AMR) AF: 0.0997 AC: 1525 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1741 AN: 5174

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4828

European-Finnish (FIN) AF: 0.0638 AC: 677 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0662 AC: 4502 AN: 68000

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.103 Hom.: 171

Bravo AF: 0.117

Asia WGS AF: 0.288 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.025
DANN	Benign	0.71
PhyloP100		-2.3
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: rs10499858; hg19: chr7-80235846;