7-80601491-G-C

Variant names:

• chr7-80601491-G-C
• rs2065666
• ENST00000435819.5:c.-183-44597G>C

Variant summary

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

The ENST00000435819.5(CD36):​c.-183-44597G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,842 control chromosomes in the GnomAD database, including 8,236 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 0.32 (8236 hom., cov: 32)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 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.-183-44597G>C		intron_variant	Intron 4 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49148 AN: 151724 Hom.: 8225 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.324 AC: 49184 AN: 151842 Hom.: 8236 Cov.: 32 AF XY: 0.326 AC XY: 24210 AN XY: 74234

African (AFR) AF: 0.272 AC: 11243 AN: 41404

American (AMR) AF: 0.260 AC: 3964 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1228 AN: 5156

South Asian (SAS) AF: 0.445 AC: 2149 AN: 4824

European-Finnish (FIN) AF: 0.379 AC: 3997 AN: 10534

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24195 AN: 67894

Other (OTH) AF: 0.327 AC: 688 AN: 2104

Alfa AF: 0.181 Hom.: 345

Bravo AF: 0.309

Asia WGS AF: 0.343 AC: 1188 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.75
PhyloP100		0.073
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: rs2065666; hg19: chr7-80230807;