ENST00000309881.11:c.-184+20823T>G

Variant names:

• chr7-80623202-T-G
• rs4545029
• ENST00000309881.11:c.-184+20823T>G

Variant summary

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

The ENST00000309881.11(CD36):​c.-184+20823T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,908 control chromosomes in the GnomAD database, including 17,219 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 (17219 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-184+20823T>G		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-180+20823T>G		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-184+20823T>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.-184+20823T>G		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-22886T>G		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-109+20823T>G		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70526 AN: 151790 Hom.: 17213 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.464 AC: 70554 AN: 151908 Hom.: 17219 Cov.: 31 AF XY: 0.461 AC XY: 34243 AN XY: 74246

African (AFR) AF: 0.336 AC: 13920 AN: 41410

American (AMR) AF: 0.510 AC: 7787 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1875 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5162

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4816

European-Finnish (FIN) AF: 0.530 AC: 5587 AN: 10536

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36745 AN: 67942

Other (OTH) AF: 0.483 AC: 1017 AN: 2104

Alfa AF: 0.515 Hom.: 75057

Bravo AF: 0.465

Asia WGS AF: 0.286 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.74
PhyloP100		-0.080
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: rs4545029; hg19: chr7-80252518; COSMIC: COSV59214997; COSMIC: COSV59214997;