rs2366855

chr7-80624139-T-Achr7-80624139-T-C

Variant summary

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

The ENST00000309881.11(CD36):c.-184+21760T>A 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 152,054 control chromosomes in the GnomAD database, including 16,727 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 0.45 (16726 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001371077.1	c.-235T>A		5_prime_UTR_variant	1/15
CD36	NM_001371078.1	c.-235T>A		5_prime_UTR_variant	1/14
CD36	XM_047421041.1	c.-573T>A		5_prime_UTR_variant	1/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-184+21760T>A		intron_variant		1		P1
CD36	ENST00000438020.5	c.-235T>A		5_prime_UTR_variant	1/5	2
CD36	ENST00000435819.5	c.-183-21949T>A		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69088 AN: 151932 Hom.: 16724 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.484

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.455 AC: 69110 AN: 152050 Hom.: 16726 Cov.: 32 AF XY: 0.452 AC XY: 33583 AN XY: 74344

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.479

Alfa AF: 0.390 Hom.: 1189

Bravo AF: 0.453

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.0
Dann	Benign	0.63

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: rs2366855; hg19: chr7-80253455;