chr7-80633685-C-T

Variant names:

• chr7-80633685-C-T
• rs9784998
• ENST00000309881.11:c.-183-12403C>T

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-12403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,838 control chromosomes in the GnomAD database, including 1,809 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 0.13 (1809 hom., cov: 32)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.03
• Publications: 8 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	XM_047421048.1	c.-1576C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 16		XP_047277004.1
CD36	XM_047421048.1	c.-1576C>T		5_prime_UTR_variant	Exon 1 of 16		XP_047277004.1
CD36	NM_001001547.3	c.-183-12403C>T		intron_variant	Intron 1 of 13		NP_001001547.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-183-12403C>T		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-12403C>T		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-108-22855C>T		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19595 AN: 151720 Hom.: 1806 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.129 AC: 19622 AN: 151838 Hom.: 1809 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74190

African (AFR) AF: 0.219 AC: 9068 AN: 41402

American (AMR) AF: 0.105 AC: 1596 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0691 AC: 240 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1745 AN: 5142

South Asian (SAS) AF: 0.241 AC: 1158 AN: 4812

European-Finnish (FIN) AF: 0.0671 AC: 708 AN: 10556

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4829 AN: 67914

Other (OTH) AF: 0.116 AC: 243 AN: 2102

Alfa AF: 0.0742 Hom.: 131

Bravo AF: 0.131

Asia WGS AF: 0.289 AC: 997 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.045
DANN	Benign	0.46
PhyloP100		-6.0
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: rs9784998; hg19: chr7-80263001;