rs9827878
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001353108.3(CEP63):āc.63T>Cā(p.Cys21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,612,436 control chromosomes in the GnomAD database, including 22,464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.16 ( 1922 hom., cov: 31)
Exomes š: 0.17 ( 20542 hom. )
Consequence
CEP63
NM_001353108.3 synonymous
NM_001353108.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.66
Genes affected
CEP63 (HGNC:25815): (centrosomal protein 63) This gene encodes a protein with six coiled-coil domains. The protein is localized to the centrosome, a non-membraneous organelle that functions as the major microtubule-organizing center in animal cells. Several alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 3-134507127-T-C is Benign according to our data. Variant chr3-134507127-T-C is described in ClinVar as [Benign]. Clinvar id is 128712.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.65 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEP63 | NM_001353108.3 | c.63T>C | p.Cys21= | synonymous_variant | 3/15 | ENST00000675561.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEP63 | ENST00000675561.1 | c.63T>C | p.Cys21= | synonymous_variant | 3/15 | NM_001353108.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23833AN: 151820Hom.: 1919 Cov.: 31
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GnomAD3 exomes AF: 0.171 AC: 42982AN: 251218Hom.: 3889 AF XY: 0.169 AC XY: 22999AN XY: 135798
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GnomAD4 exome AF: 0.166 AC: 241908AN: 1460498Hom.: 20542 Cov.: 32 AF XY: 0.166 AC XY: 120377AN XY: 726608
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GnomAD4 genome ? AF: 0.157 AC: 23840AN: 151938Hom.: 1922 Cov.: 31 AF XY: 0.159 AC XY: 11788AN XY: 74222
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 15, 2013 | - - |
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