7-80602188-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000309881.11(CD36):c.-375G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,940 control chromosomes in the GnomAD database, including 22,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.53 ( 22221 hom., cov: 32)
Exomes 𝑓: 0.39 ( 0 hom. )
Consequence
CD36
ENST00000309881.11 5_prime_UTR
ENST00000309881.11 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0130
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 7-80602188-G-C is Benign according to our data. Variant chr7-80602188-G-C is described in ClinVar as [Benign]. Clinvar id is 360740.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD36 | NM_001001547.3 | upstream_gene_variant | NP_001001547.1 | |||||
CD36 | NM_001289911.2 | upstream_gene_variant | NP_001276840.1 | |||||
CD36 | NM_001371074.1 | upstream_gene_variant | NP_001358003.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD36 | ENST00000309881.11 | c.-375G>C | 5_prime_UTR_variant | 1/14 | 1 | ENSP00000308165 | P1 | |||
CD36 | ENST00000435819.5 | c.-183-43900G>C | intron_variant | 2 | ENSP00000399421 | P1 | ||||
CD36 | ENST00000480599.6 | n.39G>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.528 AC: 80118AN: 151804Hom.: 22183 Cov.: 32
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GnomAD4 exome AF: 0.389 AC: 7AN: 18Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 4AN XY: 12
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GnomAD4 genome AF: 0.528 AC: 80205AN: 151922Hom.: 22221 Cov.: 32 AF XY: 0.531 AC XY: 39426AN XY: 74240
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Platelet-type bleeding disorder 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at