rs59637606

Positions:

• chr7-80623491-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+21112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 17,676 control chromosomes in the GnomAD database, including 55 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 0.069 (55 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-184+21112A>G		intron_variant			NP_001001547.1
CD36	NM_001289911.2	c.-109+21112A>G		intron_variant			NP_001276840.1
CD36	NM_001371074.1	c.-180+21112A>G		intron_variant			NP_001358003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-184+21112A>G		intron_variant		1		ENSP00000308165	P1
CD36	ENST00000435819.5	c.-183-22597A>G		intron_variant		2		ENSP00000399421	P1
CD36	ENST00000534394.5	c.-109+21112A>G		intron_variant		2		ENSP00000431296

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 1208 AN: 17626 Hom.: 55 Cov.: 31

Gnomad AFR AF: 0.00926

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.00483

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000922

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0686 AC: 1213 AN: 17676 Hom.: 55 Cov.: 31 AF XY: 0.0748 AC XY: 644 AN XY: 8604

Gnomad4 AFR AF: 0.00920

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.00483

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000922

Gnomad4 OTH AF: 0.109

Alfa AF: 0.00548 Hom.: 6

Bravo AF: 0.0116

Asia WGS AF: 0.0520 AC: 175 AN: 3386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.083
DANN	Benign	0.73

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: rs59637606; hg19: chr7-80252807;