chr5-55231429-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_021147.5(CCNO):c.999C>T(p.His333=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CCNO
NM_021147.5 synonymous
NM_021147.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.191
Genes affected
CCNO (HGNC:18576): (cyclin O) This gene encodes a member of the cyclin protein family, and the encoded protein is involved in regulation of the cell cycle. Disruption of this gene is associated with primary ciliary dyskinesia-19. Alternative splicing results in multiple transcript variants. This gene, which has a previous symbol of UNG2, was erroneously identified as a uracil DNA glycosylase in PubMed ID: 2001396. A later publication, PubMed ID: 8419333, identified this gene's product as a cyclin protein family member. The UNG2 symbol is also used as a specific protein isoform name for the UNG gene (GeneID 7374), so confusion exists in the scientific literature and in some databases for these two genes. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 5-55231429-G-A is Benign according to our data. Variant chr5-55231429-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 696778.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.191 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNO | NM_021147.5 | c.999C>T | p.His333= | synonymous_variant | 3/3 | ENST00000282572.5 | |
CCNO | NR_125346.2 | n.1460C>T | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125347.2 | n.1089C>T | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125348.1 | n.1063C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNO | ENST00000282572.5 | c.999C>T | p.His333= | synonymous_variant | 3/3 | 1 | NM_021147.5 | P1 | |
CCNO | ENST00000501463.2 | c.*979C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251366Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135898
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727230
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2018 | - - |
CCNO-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 17, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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