chr15-48805535-C-CT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000380950.7(CEP152):c.87+27_87+28insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,198,422 control chromosomes in the GnomAD database, including 2,446 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 2291 hom., cov: 26)
Exomes 𝑓: 0.13 ( 155 hom. )
Consequence
CEP152
ENST00000380950.7 intron
ENST00000380950.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.181
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 Benign. Variant got -10 ACMG points.
BP6
Variant 15-48805535-C-CT is Benign according to our data. Variant chr15-48805535-C-CT is described in ClinVar as [Benign]. Clinvar id is 1278089.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP152 | NM_001194998.2 | c.87+27_87+28insA | 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+27_87+28insA | intron_variant | 1 | NM_001194998.2 | ENSP00000370337 | A2 |
Frequencies
GnomAD3 genomes AF: 0.202 AC: 22454AN: 111376Hom.: 2287 Cov.: 26
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GnomAD3 exomes AF: 0.164 AC: 16145AN: 98152Hom.: 69 AF XY: 0.160 AC XY: 8593AN XY: 53738
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GnomAD4 exome AF: 0.133 AC: 144730AN: 1087034Hom.: 155 Cov.: 24 AF XY: 0.132 AC XY: 71997AN XY: 543514
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GnomAD4 genome AF: 0.202 AC: 22461AN: 111388Hom.: 2291 Cov.: 26 AF XY: 0.213 AC XY: 11508AN XY: 54072
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2019 | - - |
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