rs62461694

Positions:

• chr7-80623737-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD36	NM_001001547.3	c.-184+21358T>C		intron_variant			NP_001001547.1
CD36	NM_001371074.1	c.-180+21358T>C		intron_variant			NP_001358003.1
CD36	NM_001371075.1	c.-184+21358T>C		intron_variant			NP_001358004.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000309881.11	c.-184+21358T>C		intron_variant		1		ENSP00000308165.7
CD36	ENST00000435819.5	c.-183-22351T>C		intron_variant		2		ENSP00000399421.1
CD36	ENST00000534394.5	c.-109+21358T>C		intron_variant		2		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

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0530

Gnomad4 SAS AF: 0.0625

Gnomad4 FIN AF: 0.0849

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0608 Hom.: 35

Bravo AF: 0.0509

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs62461694; hg19: chr7-80253053;