rs1049673

Positions:

• chr7-80677034-C-G
• chr7-80677034-C-T

Variant summary

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

The NM_001001548.3(CD36):​c.*651C>G variant causes a 3 prime UTR 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 NM_001001548.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD36	NM_001001548.3	c.*651C>G		3_prime_UTR_variant	15/15	ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.*651C>G		3_prime_UTR_variant	15/15	5	NM_001001548.3	P1
CD36	ENST00000464213.1	n.3936C>G		non_coding_transcript_exon_variant	5/5	1

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

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

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.395

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1049673; hg19: chr7-80306350;