7-80584195-T-C

Variant names:

• chr7-80584195-T-C
• rs1524598
• ENST00000435819.5:c.-184+37928T>C

Variant summary

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

The ENST00000435819.5(CD36):​c.-184+37928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,248 control chromosomes in the GnomAD database, including 6,321 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 0.26 (6321 hom., cov: 33)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• 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 = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000435819.5	c.-184+37928T>C		intron_variant	Intron 4 of 16	2		ENSP00000399421.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39778 AN: 152130 Hom.: 6323 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.261 AC: 39761 AN: 152248 Hom.: 6321 Cov.: 33 AF XY: 0.256 AC XY: 19065 AN XY: 74446

African (AFR) AF: 0.107 AC: 4461 AN: 41582

American (AMR) AF: 0.252 AC: 3850 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3470

East Asian (EAS) AF: 0.00366 AC: 19 AN: 5186

South Asian (SAS) AF: 0.275 AC: 1330 AN: 4828

European-Finnish (FIN) AF: 0.290 AC: 3076 AN: 10596

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24616 AN: 67978

Other (OTH) AF: 0.309 AC: 652 AN: 2112

Alfa AF: 0.185 Hom.: 400

Bravo AF: 0.249

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		-0.51
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: rs1524598; hg19: chr7-80213511;