rs3173804

Positions:

• chr7-80670534-T-A
• chr7-80670534-T-C
• chr7-80670534-T-G

Variant summary

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

The NM_001001548.3(CD36):​c.819-443T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 211,616 control chromosomes in the GnomAD database, including 16,919 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 0.38 (11574 hom., cov: 32)
  • Exomes 𝑓: 0.41 (5345 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001548.3	c.819-443T>A		intron_variant		ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.819-443T>A		intron_variant		5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57919 AN: 151894 Hom.: 11567 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.411 AC: 24489 AN: 59604 Hom.: 5345 Cov.: 0 AF XY: 0.413 AC XY: 12856 AN XY: 31092

Gnomad4 AFR exome AF: 0.211

Gnomad4 AMR exome AF: 0.345

Gnomad4 ASJ exome AF: 0.435

Gnomad4 EAS exome AF: 0.418

Gnomad4 SAS exome AF: 0.424

Gnomad4 FIN exome AF: 0.411

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.381 AC: 57940 AN: 152012 Hom.: 11574 Cov.: 32 AF XY: 0.381 AC XY: 28317 AN XY: 74294

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.397

Alfa AF: 0.310 Hom.: 945

Bravo AF: 0.367

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.65

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: rs3173804; hg19: chr7-80299850;