rs3211816

Variant names:

• chr7-80648674-G-A
• rs3211816
• NM_001001548.3:c.120+1814G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001548.3(CD36):​c.120+1814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,688 control chromosomes in the GnomAD database, including 7,736 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 0.31 (7736 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.55
• Publications: 10 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.120+1814G>A		intron_variant	Intron 3 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.120+1814G>A		intron_variant	Intron 3 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46253 AN: 151570 Hom.: 7737 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.305 AC: 46269 AN: 151688 Hom.: 7736 Cov.: 32 AF XY: 0.309 AC XY: 22940 AN XY: 74144

African (AFR) AF: 0.170 AC: 7049 AN: 41426

American (AMR) AF: 0.326 AC: 4957 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1112 AN: 3460

East Asian (EAS) AF: 0.343 AC: 1766 AN: 5144

South Asian (SAS) AF: 0.457 AC: 2196 AN: 4810

European-Finnish (FIN) AF: 0.385 AC: 4039 AN: 10496

Middle Eastern (MID) AF: 0.385 AC: 111 AN: 288

European-Non Finnish (NFE) AF: 0.353 AC: 23949 AN: 67838

Other (OTH) AF: 0.316 AC: 664 AN: 2100

Alfa AF: 0.301 Hom.: 1094

Bravo AF: 0.292

Asia WGS AF: 0.382 AC: 1324 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.083
DANN	Benign	0.52
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3211816; hg19: chr7-80277990;