rs7755

Positions:

• chr7-80676955-G-A

Variant summary

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

The NM_001001548.3(CD36):​c.*572G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,944 control chromosomes in the GnomAD database, including 11,586 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 (11586 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CD36 NM_001001548.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773

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=-0.84).
• 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.*572G>A		3_prime_UTR_variant	15/15	ENST00000447544.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD36	ENST00000447544.7	c.*572G>A		3_prime_UTR_variant	15/15	5	NM_001001548.3	P1
CD36	ENST00000464213.1	n.3857G>A		non_coding_transcript_exon_variant	5/5	1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57571 AN: 151826 Hom.: 11582 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.393

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: 0.379 AC: 57586 AN: 151944 Hom.: 11586 Cov.: 32 AF XY: 0.380 AC XY: 28178 AN XY: 74238

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.398

Alfa AF: 0.421 Hom.: 8275

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7755; hg19: chr7-80306271;