chr3-129172608-ACAGGCAGACAGGCAGC-A

Position:

• chr3-129172608-ACAGGCAGACAGGCAGC-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BS1 BS2

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 (no stars).

• Frequency: Genomes: 𝑓 0.0023 (0 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 -9 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 no_assertion_criteria_provided, 0 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 GnomAd4 at 74 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: 73 AN: 31708 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00631

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.00250

Gnomad FIN AF: 0.00139

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000102

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00233 AC: 74 AN: 31780 Hom.: 0 Cov.: 0 AF XY: 0.00260 AC XY: 40 AN XY: 15366

Gnomad4 AFR AF: 0.000428

Gnomad4 AMR AF: 0.00628

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.00247

Gnomad4 FIN AF: 0.00139

Gnomad4 NFE AF: 0.000102

Gnomad4 OTH AF: 0.00266

Alfa AF: 0.00910 Hom.: 0

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

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: 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: rs1198962230; hg19: chr3-128891451;