rs4731642

Variant names:

• chr7-80618685-A-G
• rs4731642
• ENST00000309881.11:c.-184+16306A>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+16306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,124 control chromosomes in the GnomAD database, including 10,187 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 (10187 hom., cov: 33)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-184+16306A>G		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-180+16306A>G		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-184+16306A>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+16306A>G		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-27403A>G		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-109+16306A>G		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49365 AN: 152006 Hom.: 10184 Cov.: 33

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.325 AC: 49376 AN: 152124 Hom.: 10187 Cov.: 33 AF XY: 0.322 AC XY: 23904 AN XY: 74340

African (AFR) AF: 0.0840 AC: 3491 AN: 41560

American (AMR) AF: 0.406 AC: 6192 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3468

East Asian (EAS) AF: 0.166 AC: 854 AN: 5146

South Asian (SAS) AF: 0.166 AC: 800 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4245 AN: 10568

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31096 AN: 67982

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.373 Hom.: 4110

Bravo AF: 0.320

Asia WGS AF: 0.165 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.43
PhyloP100		0.24
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: rs4731642; hg19: chr7-80248001;