chr7-80590626-A-G

Position:

• chr7-80590626-A-G

Variant summary

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

The ENST00000435819.5(CD36):​c.-184+44359A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,824 control chromosomes in the GnomAD database, including 8,516 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 0.33 (8516 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+44359A>G		intron_variant		2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50372 AN: 151706 Hom.: 8508 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.332 AC: 50404 AN: 151824 Hom.: 8516 Cov.: 32 AF XY: 0.333 AC XY: 24680 AN XY: 74196

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.331

Alfa AF: 0.323 Hom.: 1338

Bravo AF: 0.321

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
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: rs2030711; hg19: chr7-80219942;