rs6960369

Variant names:

• chr7-80620003-G-A
• rs6960369
• ENST00000309881.11:c.-184+17624G>A

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+17624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,148 control chromosomes in the GnomAD database, including 2,479 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 0.15 (2479 hom., cov: 32)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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: 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001547.3		c.-184+17624G>A		intron	N/A	NP_001001547.1
	CD36	NM_001371074.1		c.-180+17624G>A		intron	N/A	NP_001358003.1
	CD36	NM_001371075.1		c.-184+17624G>A		intron	N/A	NP_001358004.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000309881.11	TSL:1	c.-184+17624G>A		intron	N/A	ENSP00000308165.7
	CD36	ENST00000435819.5	TSL:2	c.-183-26085G>A		intron	N/A	ENSP00000399421.1
	CD36	ENST00000534394.5	TSL:2	c.-109+17624G>A		intron	N/A	ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22233 AN: 152030 Hom.: 2475 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.146 AC: 22264 AN: 152148 Hom.: 2479 Cov.: 32 AF XY: 0.147 AC XY: 10938 AN XY: 74406

African (AFR) AF: 0.278 AC: 11528 AN: 41464

American (AMR) AF: 0.112 AC: 1710 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1733 AN: 5164

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4824

European-Finnish (FIN) AF: 0.0669 AC: 710 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4846 AN: 68004

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.116 Hom.: 195

Bravo AF: 0.150

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.21
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs6960369; hg19: chr7-80249319;