rs17154233

Variant names:

• chr7-80663873-A-C
• rs17154233
• NM_001001548.3:c.610-533A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000072.3(CD36):​c.610-533A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 152,246 control chromosomes in the GnomAD database, including 103 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 0.013 (103 hom., cov: 32)
• Consequence: CD36 NM_000072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 3 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: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000072.3. 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.610-533A>C		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.610-533A>C		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.610-533A>C		intron	N/A	NP_001001547.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.610-533A>C		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.610-533A>C		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.610-533A>C		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1932 AN: 152128 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00255

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00340

Gnomad OTH AF: 0.00957

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0127 AC: 1940 AN: 152246 Hom.: 103 Cov.: 32 AF XY: 0.0161 AC XY: 1195 AN XY: 74414

African (AFR) AF: 0.00132 AC: 55 AN: 41580

American (AMR) AF: 0.00255 AC: 39 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.144 AC: 744 AN: 5178

South Asian (SAS) AF: 0.109 AC: 525 AN: 4822

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00340 AC: 231 AN: 67986

Other (OTH) AF: 0.0170 AC: 36 AN: 2112

Alfa AF: 0.00474 Hom.: 0

Bravo AF: 0.00834

Asia WGS AF: 0.146 AC: 504 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism (auto)

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: rs17154233; hg19: chr7-80293189;