rs3211821

Variant names:

• chr7-80649247-A-G
• rs3211821
• NM_001001548.3:c.120+2387A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-80649247-A-G
• chr7-80649247-A-T

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+2387A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,856 control chromosomes in the GnomAD database, including 17,827 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 0.47 (17827 hom., cov: 31)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.120+2387A>G		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+2387A>G		intron_variant	Intron 3 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71619 AN: 151738 Hom.: 17821 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.472 AC: 71654 AN: 151856 Hom.: 17827 Cov.: 31 AF XY: 0.469 AC XY: 34771 AN XY: 74206

African (AFR) AF: 0.336 AC: 13923 AN: 41460

American (AMR) AF: 0.518 AC: 7880 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1966 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1661 AN: 5154

South Asian (SAS) AF: 0.298 AC: 1439 AN: 4822

European-Finnish (FIN) AF: 0.531 AC: 5594 AN: 10544

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37522 AN: 67872

Other (OTH) AF: 0.499 AC: 1051 AN: 2106

Alfa AF: 0.504 Hom.: 2756

Bravo AF: 0.473

Asia WGS AF: 0.297 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.085
DANN	Benign	0.49
PhyloP100		-1.6
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: rs3211821; hg19: chr7-80278563;