5-55231533-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_021147.5(CCNO):c.895C>T(p.Arg299Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,613,564 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 4 hom. )
Consequence
CCNO
NM_021147.5 missense
NM_021147.5 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 0.0140
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.011220634).
BP6
Variant 5-55231533-G-A is Benign according to our data. Variant chr5-55231533-G-A is described in ClinVar as [Benign]. Clinvar id is 2695498.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNO | NM_021147.5 | c.895C>T | p.Arg299Trp | missense_variant | 3/3 | ENST00000282572.5 | |
CCNO | NR_125346.2 | n.1356C>T | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125347.2 | n.985C>T | non_coding_transcript_exon_variant | 3/3 | |||
CCNO | NR_125348.1 | n.959C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNO | ENST00000282572.5 | c.895C>T | p.Arg299Trp | missense_variant | 3/3 | 1 | NM_021147.5 | P1 | |
CCNO | ENST00000501463.2 | c.*875C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152206Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000260 AC: 65AN: 250324Hom.: 3 AF XY: 0.000347 AC XY: 47AN XY: 135638
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GnomAD4 exome AF: 0.000138 AC: 202AN: 1461240Hom.: 4 Cov.: 31 AF XY: 0.000188 AC XY: 137AN XY: 726968
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152324Hom.: 1 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of disorder (P = 0.0317);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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