rs7755

Variant names:

• chr7-80676955-G-A
• rs7755
• NM_001001548.3:c.*572G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 42 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: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001548.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.*572G>A		3_prime_UTR	Exon 15 of 15	NP_001001548.1	P16671-1
	CD36	NM_001371075.1		c.*572G>A		3_prime_UTR	Exon 15 of 15	NP_001358004.1	P16671-1
	CD36	NM_001371077.1		c.*572G>A		3_prime_UTR	Exon 15 of 15	NP_001358006.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.*572G>A		3_prime_UTR	Exon 15 of 15	ENSP00000415743.2	P16671-1
	CD36	ENST00000464213.1	TSL:1	n.3857G>A		non_coding_transcript_exon	Exon 5 of 5
	CD36	ENST00000855923.1		c.*572G>A		3_prime_UTR	Exon 16 of 16	ENSP00000525982.1

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

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

African (AFR) AF: 0.231 AC: 9577 AN: 41470

American (AMR) AF: 0.351 AC: 5356 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2733 AN: 5156

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4822

European-Finnish (FIN) AF: 0.447 AC: 4702 AN: 10514

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30121 AN: 67952

Other (OTH) AF: 0.398 AC: 839 AN: 2110

Alfa AF: 0.420 Hom.: 13196

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7755; hg19: chr7-80306271;