7-80453698-C-G

Variant names:

• chr7-80453698-C-G
• rs799975
• ENST00000435819.5:c.-477-32769C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435819.5(CD36):​c.-477-32769C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,130 control chromosomes in the GnomAD database, including 45,282 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 0.77 (45282 hom., cov: 33)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 2 publications found

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]

CD36 Gene-Disease associations (from GenCC):

• platelet-type bleeding disorder 10

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435819.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000435819.5	TSL:2	c.-477-32769C>G		intron	N/A	ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117041 AN: 152012 Hom.: 45247 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.770 AC: 117126 AN: 152130 Hom.: 45282 Cov.: 33 AF XY: 0.774 AC XY: 57546 AN XY: 74348

African (AFR) AF: 0.827 AC: 34345 AN: 41514

American (AMR) AF: 0.776 AC: 11858 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3468

East Asian (EAS) AF: 0.796 AC: 4119 AN: 5174

South Asian (SAS) AF: 0.747 AC: 3599 AN: 4816

European-Finnish (FIN) AF: 0.812 AC: 8589 AN: 10578

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49911 AN: 67978

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.686 Hom.: 2015

Bravo AF: 0.768

Asia WGS AF: 0.781 AC: 2711 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.33
PhyloP100		-0.048
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs799975; hg19: chr7-80083014;