rs11971740

chr7-80616605-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000309881.11(CD36):c.-184+14226A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,092 control chromosomes in the GnomAD database, including 2,395 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 0.14 (2395 hom., cov: 31)
• Consequence: CD36 ENST00000309881.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.14).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001547.3	c.-184+14226A>G		intron_variant
CD36	NM_001289911.2	c.-109+14226A>G		intron_variant
CD36	NM_001371074.1	c.-180+14226A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000309881.11	c.-184+14226A>G		intron_variant		1		P1
CD36	ENST00000435819.5	c.-183-29483A>G		intron_variant		2		P1
CD36	ENST00000534394.5	c.-109+14226A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21860 AN: 151974 Hom.: 2390 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.0667

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.144 AC: 21888 AN: 152092 Hom.: 2395 Cov.: 31 AF XY: 0.145 AC XY: 10747 AN XY: 74336

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.0667

Gnomad4 NFE AF: 0.0712

Gnomad4 OTH AF: 0.126

Alfa AF: 0.104 Hom.: 296

Bravo AF: 0.148

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.015
Dann	Benign	0.28

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

Publications

LitVar

Other links and lift over

dbSNP: rs11971740; hg19: chr7-80245921;