Variant 5-55232565-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_021147.5(CCNO):c.382-19C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,611,804 control chromosomes in the GnomAD database, including 22,099 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2352 hom., cov: 33)

Exomes 𝑓: 0.16 ( 19747 hom. )

Consequence

CCNO
NM_021147.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0260

Variant links:

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]

CCNO links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 5-55232565-G-C is Benign according to our data. Variant chr5-55232565-G-C is described in ClinVar as [Benign]. Clinvar id is 261408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-55232565-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CCNO	NM_021147.5 linkuse as main transcript	c.382-19C>G	intron_variant		ENST00000282572.5
CCNO	NR_125348.1 linkuse as main transcript	n.427C>G	non_coding_transcript_exon_variant	1/2
CCNO	NR_125346.2 linkuse as main transcript	n.843-19C>G	intron_variant, non_coding_transcript_variant
CCNO	NR_125347.2 linkuse as main transcript	n.472-19C>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNO	ENST00000282572.5 linkuse as main transcript	c.382-19C>G		intron_variant		1	NM_021147.5	P1	P22674-1
CCNO	ENST00000501463.2 linkuse as main transcript	c.*362-19C>G		intron_variant, NMD_transcript_variant		1			P22674-2

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26671

AN:

152142

Hom.:

2351

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.179

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.176

GnomAD3 exomes

AF:

0.177

AC:

43588

AN:

245704

Hom.:

4011

AF XY:

0.172

AC XY:

23003

AN XY:

133838

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.213

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.179

Gnomad SAS exome

AF:

0.152

Gnomad FIN exome

AF:

0.263

Gnomad NFE exome

AF:

0.160

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.162

AC:

235971

AN:

1459544

Hom.:

19747

Cov.:

AF XY:

0.161

AC XY:

116545

AN XY:

726090

show subpopulations

Gnomad4 AFR exome

AF:

0.199

Gnomad4 AMR exome

AF:

0.206

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.174

Gnomad4 SAS exome

AF:

0.147

Gnomad4 FIN exome

AF:

0.261

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.157

GnomAD4 genome

AF:

0.175

AC:

26694

AN:

152260

Hom.:

2352

Cov.:

AF XY:

0.180

AC XY:

13422

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.267

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.104

Hom.:

211

Bravo

AF:

0.172

Asia WGS

AF:

0.171

AC:

595

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

9.3

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over