rs12531609

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000309881.11(CD36):​c.-184+9884A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0085 in 152,342 control chromosomes in the GnomAD database, including 59 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 0.0085 ( 59 hom., cov: 33)

Consequence

CD36
ENST00000309881.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.585
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.0987 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD36NM_001001547.3 linkuse as main transcriptc.-184+9884A>T intron_variant NP_001001547.1
CD36NM_001289911.2 linkuse as main transcriptc.-109+9884A>T intron_variant NP_001276840.1
CD36NM_001371074.1 linkuse as main transcriptc.-180+9884A>T intron_variant NP_001358003.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD36ENST00000309881.11 linkuse as main transcriptc.-184+9884A>T intron_variant 1 ENSP00000308165 P1P16671-1
CD36ENST00000435819.5 linkuse as main transcriptc.-183-33825A>T intron_variant 2 ENSP00000399421 P1P16671-1
CD36ENST00000534394.5 linkuse as main transcriptc.-109+9884A>T intron_variant 2 ENSP00000431296

Frequencies

GnomAD3 genomes
AF:
0.00847
AC:
1289
AN:
152224
Hom.:
59
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00147
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0367
Gnomad ASJ
AF:
0.000577
Gnomad EAS
AF:
0.106
Gnomad SAS
AF:
0.0176
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.0120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00850
AC:
1295
AN:
152342
Hom.:
59
Cov.:
33
AF XY:
0.00953
AC XY:
710
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.00147
Gnomad4 AMR
AF:
0.0369
Gnomad4 ASJ
AF:
0.000577
Gnomad4 EAS
AF:
0.106
Gnomad4 SAS
AF:
0.0178
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00434
Hom.:
6
Bravo
AF:
0.0118
Asia WGS
AF:
0.0570
AC:
197
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.0
DANN
Benign
0.73

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12531609; hg19: chr7-80241579; API