rs17263407

chr7-80630592-G-Cchr7-80630592-G-T

Variant summary

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

The ENST00000309881.11(CD36):c.-183-15496G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,802 control chromosomes in the GnomAD database, including 8,086 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 0.32 (8086 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-183-15496G>C		intron_variant
CD36	NM_001289911.2	c.-108-25948G>C		intron_variant
CD36	NM_001371074.1	c.-179-15500G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-183-15496G>C		intron_variant		1		P1
CD36	ENST00000428497.5	c.-184+4360G>C		intron_variant		3
CD36	ENST00000435819.5	c.-183-15496G>C		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48233 AN: 151684 Hom.: 8090 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.318 AC: 48238 AN: 151802 Hom.: 8086 Cov.: 31 AF XY: 0.320 AC XY: 23734 AN XY: 74182

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.326

Alfa AF: 0.182 Hom.: 351

Bravo AF: 0.303

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.6
Dann	Benign	0.45

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: rs17263407; hg19: chr7-80259908;