7-80609147-C-T

Variant names:

• chr7-80609147-C-T
• rs1761662
• ENST00000309881.11:c.-184+6768C>T

Variant summary

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

The NM_001001547.3(CD36):​c.-184+6768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,888 control chromosomes in the GnomAD database, including 23,597 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 0.54 (23597 hom., cov: 31)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 3 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001547.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001547.3		c.-184+6768C>T		intron	N/A	NP_001001547.1	P16671-1
	CD36	NM_001371074.1		c.-180+6768C>T		intron	N/A	NP_001358003.1	P16671-1
	CD36	NM_001371075.1		c.-184+6768C>T		intron	N/A	NP_001358004.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+6768C>T		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000435819.5	TSL:2	c.-183-36941C>T		intron	N/A	ENSP00000399421.1	P16671-1
	CD36	ENST00000855923.1		c.-183-36941C>T		intron	N/A	ENSP00000525982.1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82331 AN: 151774 Hom.: 23556 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.543 AC: 82421 AN: 151888 Hom.: 23597 Cov.: 31 AF XY: 0.545 AC XY: 40427 AN XY: 74210

African (AFR) AF: 0.719 AC: 29785 AN: 41422

American (AMR) AF: 0.447 AC: 6820 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3513 AN: 5142

South Asian (SAS) AF: 0.712 AC: 3422 AN: 4804

European-Finnish (FIN) AF: 0.466 AC: 4906 AN: 10522

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30711 AN: 67948

Other (OTH) AF: 0.516 AC: 1085 AN: 2102

Alfa AF: 0.485 Hom.: 8071

Bravo AF: 0.541

Asia WGS AF: 0.715 AC: 2483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.23
PhyloP100		0.25
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: rs1761662; hg19: chr7-80238463;