rs3211931

Variant names:

• chr7-80668857-C-T
• rs3211931
• NM_001001548.3:c.749-1096C>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.749-1096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,984 control chromosomes in the GnomAD database, including 11,772 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 0.38 (11772 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 22 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.749-1096C>T		intron_variant	Intron 8 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.749-1096C>T		intron_variant	Intron 8 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58386 AN: 151868 Hom.: 11762 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.384 AC: 58418 AN: 151984 Hom.: 11772 Cov.: 32 AF XY: 0.385 AC XY: 28601 AN XY: 74264

African (AFR) AF: 0.256 AC: 10604 AN: 41488

American (AMR) AF: 0.353 AC: 5387 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2660 AN: 5160

South Asian (SAS) AF: 0.459 AC: 2209 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4700 AN: 10534

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30036 AN: 67950

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.426 Hom.: 55176

Bravo AF: 0.369

Asia WGS AF: 0.494 AC: 1715 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.55
PhyloP100		-0.79
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: rs3211931; hg19: chr7-80298173;