7-80643252-T-C

Variant names:

• chr7-80643252-T-C
• rs1527479
• NM_001001548.3:c.-183-2836T>C

Variant summary

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

The NM_001001548.3(CD36):​c.-183-2836T>C 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 151,980 control chromosomes in the GnomAD database, including 16,975 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 (16975 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 39 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001548.3. 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
	CD36	NM_001001548.3	MANE Select	c.-183-2836T>C		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.-183-2836T>C		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.-183-2836T>C		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.-183-2836T>C		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.-183-2836T>C		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.-183-2836T>C		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69399 AN: 151862 Hom.: 16969 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.457 AC: 69428 AN: 151980 Hom.: 16975 Cov.: 32 AF XY: 0.454 AC XY: 33728 AN XY: 74286

African (AFR) AF: 0.295 AC: 12228 AN: 41442

American (AMR) AF: 0.509 AC: 7755 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1910 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1667 AN: 5164

South Asian (SAS) AF: 0.296 AC: 1429 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5604 AN: 10566

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

European-Non Finnish (NFE) AF: 0.547 AC: 37205 AN: 67960

Other (OTH) AF: 0.484 AC: 1020 AN: 2106

Alfa AF: 0.508 Hom.: 10724

Bravo AF: 0.456

Asia WGS AF: 0.294 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.44
DANN	Benign	0.75
PhyloP100		-1.3
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: rs1527479; hg19: chr7-80272568;