rs62461694

Variant names:

• chr7-80623737-T-C
• rs62461694
• ENST00000309881.11:c.-184+21358T>C

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+21358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,176 control chromosomes in the GnomAD database, including 284 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 0.054 (284 hom., cov: 33)
• Consequence: CD36 NM_001001547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0697 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+21358T>C		intron	N/A	NP_001001547.1
	CD36	NM_001371074.1		c.-180+21358T>C		intron	N/A	NP_001358003.1
	CD36	NM_001371075.1		c.-184+21358T>C		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+21358T>C		intron	N/A	ENSP00000308165.7
	CD36	ENST00000435819.5	TSL:2	c.-183-22351T>C		intron	N/A	ENSP00000399421.1
	CD36	ENST00000534394.5	TSL:2	c.-109+21358T>C		intron	N/A	ENSP00000431296.1

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8209 AN: 152058 Hom.: 285 Cov.: 33

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0539 AC: 8204 AN: 152176 Hom.: 284 Cov.: 33 AF XY: 0.0541 AC XY: 4027 AN XY: 74412

African (AFR) AF: 0.0123 AC: 510 AN: 41522

American (AMR) AF: 0.0547 AC: 836 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.0530 AC: 274 AN: 5168

South Asian (SAS) AF: 0.0625 AC: 301 AN: 4818

European-Finnish (FIN) AF: 0.0849 AC: 900 AN: 10600

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4850 AN: 67996

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.0438 Hom.: 73

Bravo AF: 0.0509

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs62461694; hg19: chr7-80253053;