rs1534314

Variant names:

• chr7-80641792-G-A
• rs1534314
• NM_001001548.3:c.-184+3046G>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.-184+3046G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,866 control chromosomes in the GnomAD database, including 2,239 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 0.14 (2239 hom., cov: 31)
• Consequence: CD36 NM_001001548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD36	NM_001001548.3	c.-184+3046G>A		intron_variant	Intron 1 of 14	ENST00000447544.7	NP_001001548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD36	ENST00000447544.7	c.-184+3046G>A		intron_variant	Intron 1 of 14	5	NM_001001548.3	ENSP00000415743.2

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21330 AN: 151750 Hom.: 2230 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.141 AC: 21370 AN: 151866 Hom.: 2239 Cov.: 31 AF XY: 0.143 AC XY: 10623 AN XY: 74240

African (AFR) AF: 0.231 AC: 9542 AN: 41392

American (AMR) AF: 0.148 AC: 2255 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0698 AC: 242 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2236 AN: 5144

South Asian (SAS) AF: 0.258 AC: 1242 AN: 4812

European-Finnish (FIN) AF: 0.0668 AC: 706 AN: 10576

Middle Eastern (MID) AF: 0.0517 AC: 15 AN: 290

European-Non Finnish (NFE) AF: 0.0712 AC: 4837 AN: 67918

Other (OTH) AF: 0.130 AC: 275 AN: 2110

Alfa AF: 0.0878 Hom.: 1116

Bravo AF: 0.146

Asia WGS AF: 0.345 AC: 1194 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.38
PhyloP100		-0.72
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: rs1534314; hg19: chr7-80271108;