ENST00000435819.5:c.-184+23A>G

Variant names:

• chr7-80546290-A-G
• rs1194197
• ENST00000435819.5:c.-184+23A>G

Variant summary

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

The ENST00000435819.5(CD36):​c.-184+23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,988 control chromosomes in the GnomAD database, including 21,660 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 0.53 (21655 hom., cov: 32)
  • Exomes 𝑓: 0.53 (5 hom.)
• Consequence: CD36 ENST00000435819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 10 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

LOC124901685 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435819.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000435819.5	TSL:2	c.-184+23A>G		intron	N/A	ENSP00000399421.1
	CD36	ENST00000648416.1		n.132+23A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80198 AN: 151840 Hom.: 21635 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.533

GnomAD4 exome AF: 0.533 AC: 16 AN: 30 Hom.: 5 Cov.: 0 AF XY: 0.538 AC XY: 14 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.577 AC: 15 AN: 26

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.528 AC: 80271 AN: 151958 Hom.: 21655 Cov.: 32 AF XY: 0.528 AC XY: 39189 AN XY: 74254

African (AFR) AF: 0.606 AC: 25097 AN: 41432

American (AMR) AF: 0.495 AC: 7548 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3475 AN: 5138

South Asian (SAS) AF: 0.711 AC: 3428 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4277 AN: 10566

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32883 AN: 67966

Other (OTH) AF: 0.536 AC: 1132 AN: 2112

Alfa AF: 0.497 Hom.: 2372

Bravo AF: 0.531

Asia WGS AF: 0.695 AC: 2413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.50
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: rs1194197; hg19: chr7-80175606;