rs1334511

Positions:

• chr7-80636752-A-G

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-9336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 151,972 control chromosomes in the GnomAD database, including 2,040 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 0.14 (2040 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

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 (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-183-9336A>G		intron_variant
CD36	NM_001289911.2	c.-108-19788A>G		intron_variant
CD36	NM_001371074.1	c.-179-9340A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-183-9336A>G		intron_variant		1		P1
CD36	ENST00000428497.5	c.-183-9336A>G		intron_variant		3
CD36	ENST00000435819.5	c.-183-9336A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20502 AN: 151854 Hom.: 2038 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.118

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.135 AC: 20528 AN: 151972 Hom.: 2040 Cov.: 32 AF XY: 0.136 AC XY: 10114 AN XY: 74304

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0817 Hom.: 700

Bravo AF: 0.137

Asia WGS AF: 0.295 AC: 1024 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	5.2
DANN	Benign	0.77

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: rs1334511; hg19: chr7-80266068;