ENST00000464213.1:n.3936C>G

Variant names:

• chr7-80677034-C-G
• rs1049673
• ENST00000464213.1:n.3936C>G

Variant summary

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

The ENST00000464213.1(CD36):​n.3936C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,004 control chromosomes in the GnomAD database, including 11,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as no classification for the single variant (no stars).

• Frequency:
  • Genomes: 𝑓 0.37 (11441 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CD36 ENST00000464213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 32 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464213.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.*651C>G		3_prime_UTR	Exon 15 of 15	NP_001001548.1
	CD36	NM_001371075.1		c.*651C>G		3_prime_UTR	Exon 15 of 15	NP_001358004.1
	CD36	NM_001371077.1		c.*651C>G		3_prime_UTR	Exon 15 of 15	NP_001358006.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000464213.1	TSL:1	n.3936C>G		non_coding_transcript_exon	Exon 5 of 5
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.*651C>G		3_prime_UTR	Exon 15 of 15	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56869 AN: 151886 Hom.: 11435 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.390

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.374 AC: 56886 AN: 152004 Hom.: 11441 Cov.: 32 AF XY: 0.375 AC XY: 27869 AN XY: 74318

African (AFR) AF: 0.214 AC: 8880 AN: 41462

American (AMR) AF: 0.348 AC: 5317 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2741 AN: 5172

South Asian (SAS) AF: 0.462 AC: 2231 AN: 4828

European-Finnish (FIN) AF: 0.447 AC: 4718 AN: 10544

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30128 AN: 67950

Other (OTH) AF: 0.395 AC: 832 AN: 2104

Alfa AF: 0.394 Hom.: 1483

Bravo AF: 0.356

Asia WGS AF: 0.494 AC: 1710 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1049673; hg19: chr7-80306350;