15-48805535-CTTTTTTT-CTTTTT
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The ENST00000380950.7(CEP152):c.87+26_87+27del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00236 in 1,220,676 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0026 ( 0 hom. )
Consequence
CEP152
ENST00000380950.7 intron
ENST00000380950.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.192
Genes affected
CEP152 (HGNC:29298): (centrosomal protein 152) This gene encodes a protein that is thought to be involved with centrosome function. Mutations in this gene have been associated with primary microcephaly (MCPH4). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0026 (2880/1109200) while in subpopulation AFR AF= 0.00491 (125/25456). AF 95% confidence interval is 0.00421. There are 0 homozygotes in gnomad4_exome. There are 1466 alleles in male gnomad4_exome subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.87+26_87+27del | intron_variant | ENST00000380950.7 | NP_001181927.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP152 | ENST00000380950.7 | c.87+26_87+27del | intron_variant | 1 | NM_001194998.2 | ENSP00000370337 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000538 AC: 6AN: 111476Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.00451 AC: 443AN: 98152Hom.: 0 AF XY: 0.00476 AC XY: 256AN XY: 53738
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GnomAD4 exome AF: 0.00260 AC: 2880AN: 1109200Hom.: 0 AF XY: 0.00264 AC XY: 1466AN XY: 555496
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GnomAD4 genome AF: 0.0000538 AC: 6AN: 111476Hom.: 0 Cov.: 0 AF XY: 0.0000555 AC XY: 3AN XY: 54072
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at