7-80589645-C-T

Variant names:

• chr7-80589645-C-T
• rs6961069
• ENST00000435819.5:c.-184+43378C>T

Variant summary

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

The ENST00000435819.5(CD36):​c.-184+43378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,840 control chromosomes in the GnomAD database, including 16,640 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 0.46 (16640 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+43378C>T		intron_variant	Intron 4 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69938 AN: 151724 Hom.: 16623 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.461 AC: 69991 AN: 151840 Hom.: 16640 Cov.: 32 AF XY: 0.466 AC XY: 34558 AN XY: 74218

African (AFR) AF: 0.510 AC: 21128 AN: 41434

American (AMR) AF: 0.406 AC: 6192 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1418 AN: 3460

East Asian (EAS) AF: 0.678 AC: 3495 AN: 5152

South Asian (SAS) AF: 0.707 AC: 3412 AN: 4826

European-Finnish (FIN) AF: 0.419 AC: 4415 AN: 10544

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28409 AN: 67852

Other (OTH) AF: 0.448 AC: 943 AN: 2104

Alfa AF: 0.441 Hom.: 7970

Bravo AF: 0.454

Asia WGS AF: 0.686 AC: 2383 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	1.1
DANN	Benign	0.71
PhyloP100		-0.57
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: rs6961069; hg19: chr7-80218961;