7-80672184-G-T

Variant names:

• chr7-80672184-G-T
• rs1527483
• NM_001001548.3:c.1125+144G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001001548.3(CD36):​c.1125+144G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 517,270 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000019 (0 hom.)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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.1125+144G>T		intron	N/A	NP_001001548.1	P16671-1
	CD36	NM_000072.3		c.1125+144G>T		intron	N/A	NP_000063.2	A4D1B1
	CD36	NM_001001547.3		c.1125+144G>T		intron	N/A	NP_001001547.1	P16671-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.1125+144G>T		intron	N/A	ENSP00000415743.2	P16671-1
	CD36	ENST00000309881.11	TSL:1	c.1125+144G>T		intron	N/A	ENSP00000308165.7	P16671-1
	CD36	ENST00000394788.7	TSL:1	c.1125+144G>T		intron	N/A	ENSP00000378268.3	P16671-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000193 AC: 1 AN: 517270 Hom.: 0 AF XY: 0.00000362 AC XY: 1 AN XY: 276068

African (AFR) AF: 0.00 AC: 0 AN: 13646

American (AMR) AF: 0.00 AC: 0 AN: 22322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15258

East Asian (EAS) AF: 0.00 AC: 0 AN: 29156

South Asian (SAS) AF: 0.0000217 AC: 1 AN: 46110

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28008

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2022

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 332924

Other (OTH) AF: 0.00 AC: 0 AN: 27824

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.41
PhyloP100		-0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1527483; hg19: chr7-80301500;