7-80632908-C-T

Variant names:

• chr7-80632908-C-T
• rs13438282
• ENST00000309881.11:c.-183-13180C>T

Variant summary

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

The ENST00000309881.11(CD36):​c.-183-13180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,448 control chromosomes in the GnomAD database, including 16,835 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 (16835 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-183-13180C>T		intron_variant	Intron 1 of 13		NP_001001547.1
CD36	NM_001371074.1	c.-179-13184C>T		intron_variant	Intron 1 of 13		NP_001358003.1
CD36	NM_001371075.1	c.-183-13180C>T		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.-183-13180C>T		intron_variant	Intron 1 of 13	1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-13180C>T		intron_variant	Intron 4 of 16	2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-108-23632C>T		intron_variant	Intron 1 of 11	2		ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69146 AN: 151330 Hom.: 16830 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.457 AC: 69174 AN: 151448 Hom.: 16835 Cov.: 31 AF XY: 0.454 AC XY: 33622 AN XY: 73988

African (AFR) AF: 0.304 AC: 12572 AN: 41332

American (AMR) AF: 0.507 AC: 7689 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1872 AN: 3454

East Asian (EAS) AF: 0.313 AC: 1605 AN: 5120

South Asian (SAS) AF: 0.294 AC: 1417 AN: 4814

European-Finnish (FIN) AF: 0.533 AC: 5593 AN: 10494

Middle Eastern (MID) AF: 0.514 AC: 149 AN: 290

European-Non Finnish (NFE) AF: 0.543 AC: 36804 AN: 67774

Other (OTH) AF: 0.482 AC: 1014 AN: 2104

Alfa AF: 0.506 Hom.: 7666

Bravo AF: 0.456

Asia WGS AF: 0.283 AC: 986 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.067
DANN	Benign	0.63
PhyloP100		-2.6
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: rs13438282; hg19: chr7-80262224;