7-80677435-C-T

Variant names:

• chr7-80677435-C-T
• rs13246513
• NM_001001548.3:c.*1052C>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.*1052C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,872 control chromosomes in the GnomAD database, including 11,051 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 0.37 (11051 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CD36 NM_001001548.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 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.*1052C>T		3_prime_UTR	Exon 15 of 15	NP_001001548.1	P16671-1
	CD36	NM_001371075.1		c.*1052C>T		3_prime_UTR	Exon 15 of 15	NP_001358004.1	P16671-1
	CD36	NM_001371077.1		c.*1052C>T		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.*1052C>T		3_prime_UTR	Exon 15 of 15	ENSP00000415743.2	P16671-1
	CD36	ENST00000464213.1	TSL:1	n.4337C>T		non_coding_transcript_exon	Exon 5 of 5
	CD36	ENST00000855925.1		c.*1052C>T		3_prime_UTR	Exon 15 of 15	ENSP00000525984.1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55928 AN: 151752 Hom.: 11046 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.383

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: 0.368 AC: 55940 AN: 151872 Hom.: 11051 Cov.: 32 AF XY: 0.368 AC XY: 27320 AN XY: 74218

African (AFR) AF: 0.211 AC: 8753 AN: 41440

American (AMR) AF: 0.347 AC: 5289 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1496 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2222 AN: 5128

South Asian (SAS) AF: 0.439 AC: 2111 AN: 4810

European-Finnish (FIN) AF: 0.444 AC: 4682 AN: 10534

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30052 AN: 67928

Other (OTH) AF: 0.388 AC: 816 AN: 2102

Alfa AF: 0.403 Hom.: 3342

Bravo AF: 0.352

Asia WGS AF: 0.444 AC: 1539 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs13246513; hg19: chr7-80306751;