NM_001001548.3:c.749-1549C>G

Variant names:

• chr7-80668404-C-G
• rs3211928
• NM_001001548.3:c.749-1549C>G

Variant summary

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

The NM_001001548.3(CD36):​c.749-1549C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,874 control chromosomes in the GnomAD database, including 11,880 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 0.39 (11880 hom., cov: 32)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	NM_001001548.3	MANE Select	c.749-1549C>G		intron	N/A	NP_001001548.1
	CD36	NM_000072.3		c.749-1549C>G		intron	N/A	NP_000063.2
	CD36	NM_001001547.3		c.749-1549C>G		intron	N/A	NP_001001547.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD36	ENST00000447544.7	TSL:5 MANE Select	c.749-1549C>G		intron	N/A	ENSP00000415743.2
	CD36	ENST00000309881.11	TSL:1	c.749-1549C>G		intron	N/A	ENSP00000308165.7
	CD36	ENST00000394788.7	TSL:1	c.749-1549C>G		intron	N/A	ENSP00000378268.3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58686 AN: 151756 Hom.: 11869 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.387 AC: 58717 AN: 151874 Hom.: 11880 Cov.: 32 AF XY: 0.387 AC XY: 28728 AN XY: 74202

African (AFR) AF: 0.260 AC: 10752 AN: 41410

American (AMR) AF: 0.354 AC: 5406 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2647 AN: 5112

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4702 AN: 10530

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30136 AN: 67948

Other (OTH) AF: 0.399 AC: 842 AN: 2108

Alfa AF: 0.294 Hom.: 850

Bravo AF: 0.371

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.070
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: rs3211928; hg19: chr7-80297720;