chr7-80659727-A-T

Variant names:

• chr7-80659727-A-T
• rs3211883
• NM_001001548.3:c.282-1336A>T

Variant summary

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

The NM_001001548.3(CD36):​c.282-1336A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,006 control chromosomes in the GnomAD database, including 46,434 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 0.75 (46434 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 20 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.282-1336A>T		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_000072.3		c.282-1336A>T		intron	N/A	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.282-1336A>T		intron	N/A	NP_001001547.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.282-1336A>T		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000309881.11	TSL:1	c.282-1336A>T		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000394788.7	TSL:1	c.282-1336A>T		intron	N/A	ENSP00000378268.3	P16671-1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114633 AN: 151890 Hom.: 46437 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.754 AC: 114664 AN: 152006 Hom.: 46434 Cov.: 32 AF XY: 0.755 AC XY: 56101 AN XY: 74290

African (AFR) AF: 0.448 AC: 18537 AN: 41392

American (AMR) AF: 0.801 AC: 12227 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3083 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3209 AN: 5170

South Asian (SAS) AF: 0.737 AC: 3558 AN: 4828

European-Finnish (FIN) AF: 0.914 AC: 9668 AN: 10574

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61551 AN: 67984

Other (OTH) AF: 0.792 AC: 1675 AN: 2114

Alfa AF: 0.817 Hom.: 6577

Bravo AF: 0.737

Asia WGS AF: 0.633 AC: 2198 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.079
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: rs3211883; hg19: chr7-80289043;