ENST00000309881.11:c.-183-9779T>G

Variant names:

• chr7-80636309-T-G
• rs1953299
• ENST00000309881.11:c.-183-9779T>G

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-9779T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,828 control chromosomes in the GnomAD database, including 16,735 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 0.45 (16735 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-183-9779T>G		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-179-9783T>G		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-183-9779T>G		intron_variant	Intron 1 of 14		NP_001358004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-183-9779T>G		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-9779T>G		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-108-20231T>G		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68422 AN: 151712 Hom.: 16733 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.451 AC: 68433 AN: 151828 Hom.: 16735 Cov.: 31 AF XY: 0.448 AC XY: 33248 AN XY: 74188

African (AFR) AF: 0.272 AC: 11256 AN: 41418

American (AMR) AF: 0.511 AC: 7776 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1937 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5158

South Asian (SAS) AF: 0.296 AC: 1428 AN: 4818

European-Finnish (FIN) AF: 0.529 AC: 5574 AN: 10538

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37227 AN: 67914

Other (OTH) AF: 0.477 AC: 999 AN: 2096

Alfa AF: 0.374 Hom.: 1096

Bravo AF: 0.449

Asia WGS AF: 0.283 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.21
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: rs1953299; hg19: chr7-80265625;