rs17263407
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000309881.11(CD36):c.-183-15496G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,802 control chromosomes in the GnomAD database, including 8,086 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 0.32 ( 8086 hom., cov: 31)
Consequence
CD36
ENST00000309881.11 intron
ENST00000309881.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.475
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD36 | NM_001001547.3 | c.-183-15496G>C | intron_variant | ||||
CD36 | NM_001289911.2 | c.-108-25948G>C | intron_variant | ||||
CD36 | NM_001371074.1 | c.-179-15500G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD36 | ENST00000309881.11 | c.-183-15496G>C | intron_variant | 1 | P1 | ||||
CD36 | ENST00000428497.5 | c.-184+4360G>C | intron_variant | 3 | |||||
CD36 | ENST00000435819.5 | c.-183-15496G>C | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.318 AC: 48233AN: 151684Hom.: 8090 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.318 AC: 48238AN: 151802Hom.: 8086 Cov.: 31 AF XY: 0.320 AC XY: 23734AN XY: 74182
GnomAD4 genome
?
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31
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23734
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74182
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1186
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at