3-129172600-GCAGGCAGA-G

Position:

• chr3-129172600-GCAGGCAGA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003418.5(CNBP):​c.-14-837_-14-830del 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 0.30 (3760 hom., cov: 0)
• Consequence: CNBP NM_003418.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-129172600-GCAGGCAGA-G is Benign according to our data. Variant chr3-129172600-GCAGGCAGA-G is described in ClinVar as [Likely_benign]. Clinvar id is 3042006.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNBP	NM_003418.5	c.-14-837_-14-830del		intron_variant		ENST00000422453.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNBP	ENST00000422453.7	c.-14-837_-14-830del		intron_variant		1	NM_003418.5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 14941 AN: 49664 Hom.: 3765 Cov.: 0

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.329

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.300 AC: 14935 AN: 49728 Hom.: 3760 Cov.: 0 AF XY: 0.294 AC XY: 6895 AN XY: 23484

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.322

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

CNBP-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 16, 2023

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: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55999291; hg19: chr3-128891443;