7-80650519-A-T

Variant summary

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

The NM_001001548.3(CD36):c.120+3659A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,932 control chromosomes in the GnomAD database, including 7,498 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 0.30 (7498 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.120+3659A>T		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.120+3659A>T		intron_variant		5	NM_001001548.3	P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45518 AN: 151814 Hom.: 7502 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.300 AC: 45523 AN: 151932 Hom.: 7498 Cov.: 32 AF XY: 0.303 AC XY: 22482 AN XY: 74248

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.310

Alfa AF: 0.200 Hom.: 471

Bravo AF: 0.284

Asia WGS AF: 0.332 AC: 1151 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.5
Dann	Benign	0.84

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: rs997906; hg19: chr7-80279835;