rs10499859

Variant names:

• chr7-80629494-A-G
• rs10499859
• ENST00000309881.11:c.-183-16594A>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.-183-16594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,888 control chromosomes in the GnomAD database, including 16,798 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 0.46 (16798 hom., cov: 32)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 41 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001547.3		c.-183-16594A>G		intron	N/A	NP_001001547.1	P16671-1
	CD36	NM_001371074.1		c.-179-16598A>G		intron	N/A	NP_001358003.1	P16671-1
	CD36	NM_001371075.1		c.-183-16594A>G		intron	N/A	NP_001358004.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-183-16594A>G		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000435819.5	TSL:2	c.-183-16594A>G		intron	N/A	ENSP00000399421.1	P16671-1
	CD36	ENST00000855923.1		c.-183-16594A>G		intron	N/A	ENSP00000525982.1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69157 AN: 151770 Hom.: 16795 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.455 AC: 69180 AN: 151888 Hom.: 16798 Cov.: 32 AF XY: 0.453 AC XY: 33587 AN XY: 74222

African (AFR) AF: 0.301 AC: 12473 AN: 41476

American (AMR) AF: 0.508 AC: 7714 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1625 AN: 5144

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4820

European-Finnish (FIN) AF: 0.530 AC: 5592 AN: 10556

Middle Eastern (MID) AF: 0.521 AC: 151 AN: 290

European-Non Finnish (NFE) AF: 0.542 AC: 36843 AN: 67920

Other (OTH) AF: 0.481 AC: 1011 AN: 2102

Alfa AF: 0.514 Hom.: 35564

Bravo AF: 0.455

Asia WGS AF: 0.283 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		-0.30
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: rs10499859; hg19: chr7-80258810;