rs3211960

Positions:

• chr7-80675296-A-G

Variant summary

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

The NM_001001548.3(CD36):​c.*1-1088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,562 control chromosomes in the GnomAD database, including 10,569 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 0.35 (10569 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.*1-1088A>G		intron_variant		ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.*1-1088A>G		intron_variant		5	NM_001001548.3	P1
CD36	ENST00000464213.1	n.3286-1088A>G		intron_variant, non_coding_transcript_variant		1
CD36	ENST00000488048.1	c.*1-812A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53144 AN: 151446 Hom.: 10564 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.351 AC: 53142 AN: 151562 Hom.: 10569 Cov.: 32 AF XY: 0.352 AC XY: 26062 AN XY: 74102

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.375

Alfa AF: 0.381 Hom.: 1756

Bravo AF: 0.331

Asia WGS AF: 0.452 AC: 1569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3211960; hg19: chr7-80304612;