7-80663133-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001001548.3(CD36):c.573G>A(p.Pro191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 1,613,100 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.019 ( 52 hom., cov: 32)
Exomes 𝑓: 0.024 ( 527 hom. )
Consequence
CD36
NM_001001548.3 synonymous
NM_001001548.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.528
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant 7-80663133-G-A is Benign according to our data. Variant chr7-80663133-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 910697.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=1}.
BP7
?
Synonymous conserved (PhyloP=-0.528 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0186 (2834/152158) while in subpopulation NFE AF= 0.0281 (1908/67988). AF 95% confidence interval is 0.027. There are 52 homozygotes in gnomad4. There are 1418 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 52 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD36 | NM_001001548.3 | c.573G>A | p.Pro191= | synonymous_variant | 6/15 | ENST00000447544.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD36 | ENST00000447544.7 | c.573G>A | p.Pro191= | synonymous_variant | 6/15 | 5 | NM_001001548.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2836AN: 152040Hom.: 52 Cov.: 32
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GnomAD3 exomes AF: 0.0188 AC: 4714AN: 251244Hom.: 74 AF XY: 0.0184 AC XY: 2500AN XY: 135790
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GnomAD4 exome AF: 0.0245 AC: 35771AN: 1460942Hom.: 527 Cov.: 31 AF XY: 0.0240 AC XY: 17428AN XY: 726810
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GnomAD4 genome ? AF: 0.0186 AC: 2834AN: 152158Hom.: 52 Cov.: 32 AF XY: 0.0191 AC XY: 1418AN XY: 74368
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Platelet-type bleeding disorder 10 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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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