3-129172608-ACAGGCAGACAGGCAGC-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_003418.5(CNBP):c.-14-853_-14-838del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 0 hom., cov: 0)
Consequence
CNBP
NM_003418.5 intron
NM_003418.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0750
Genes affected
CNBP (HGNC:13164): (CCHC-type zinc finger nucleic acid binding protein) This gene encodes a nucleic-acid binding protein with seven zinc-finger domains. The protein has a preference for binding single stranded DNA and RNA. The protein functions in cap-independent translation of ornithine decarboxylase mRNA, and may also function in sterol-mediated transcriptional regulation. A CCTG expansion from <30 repeats to 75-11000 repeats in the first intron of this gene results in myotonic dystrophy type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 3-129172608-ACAGGCAGACAGGCAGC-A is Benign according to our data. Variant chr3-129172608-ACAGGCAGACAGGCAGC-A is described in ClinVar as [Likely_benign]. Clinvar id is 3033016.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00233 (74/31780) while in subpopulation EAS AF= 0.034 (43/1266). AF 95% confidence interval is 0.0259. There are 0 homozygotes in gnomad4. There are 40 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High AC in GnomAd at 73 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNBP | NM_003418.5 | c.-14-853_-14-838del | intron_variant | ENST00000422453.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNBP | ENST00000422453.7 | c.-14-853_-14-838del | intron_variant | 1 | NM_003418.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00230 AC: 73AN: 31708Hom.: 0 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
73
AN:
31708
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00233 AC: 74AN: 31780Hom.: 0 Cov.: 0 AF XY: 0.00260 AC XY: 40AN XY: 15366
GnomAD4 genome
?
AF:
AC:
74
AN:
31780
Hom.:
Cov.:
0
AF XY:
AC XY:
40
AN XY:
15366
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CNBP-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 2021 | 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
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at