rs10499858

chr7-80606530-A-G

Variant summary

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

The ENST00000309881.11(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 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-184+4151A>G		intron_variant
CD36	NM_001289911.2	c.-109+4151A>G		intron_variant
CD36	NM_001371074.1	c.-180+4151A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-184+4151A>G		intron_variant		1		P1
CD36	ENST00000435819.5	c.-183-39558A>G		intron_variant		2		P1
CD36	ENST00000534394.5	c.-109+4151A>G		intron_variant		2

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.0638

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0989 Hom.: 149

Bravo AF: 0.117

Asia WGS AF: 0.288 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.025
Dann	Benign	0.71

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: rs10499858; hg19: chr7-80235846;