Variant 3-129171507-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_003418.5(CNBP):c.156C>T(p.Asp52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.933 in 1,614,018 control chromosomes in the GnomAD database, including 714,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 53563 hom., cov: 33)

Exomes 𝑓: 0.95 ( 661244 hom. )

Consequence

CNBP
NM_003418.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.97

Variant links:

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]

CNBP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-129171507-G-A is Benign according to our data. Variant chr3-129171507-G-A is described in ClinVar as [Benign]. Clinvar id is 1217358.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-129171507-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CNBP	NM_003418.5 linkuse as main transcript	c.156C>T	p.Asp52=	synonymous_variant	3/5	ENST00000422453.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CNBP	ENST00000422453.7 linkuse as main transcript	c.156C>T	p.Asp52=	synonymous_variant	3/5	1	NM_003418.5		P62633-1

Frequencies

GnomAD3 genomes

AF:

0.806

AC:

122634

AN:

152110

Hom.:

53569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.872

Gnomad ASJ

AF:

0.959

Gnomad EAS

AF:

0.887

Gnomad SAS

AF:

0.845

Gnomad FIN

AF:

0.955

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.973

Gnomad OTH

AF:

0.848

GnomAD3 exomes

AF:

0.899

AC:

226052

AN:

251466

Hom.:

103883

AF XY:

0.908

AC XY:

123391

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.426

Gnomad AMR exome

AF:

0.876

Gnomad ASJ exome

AF:

0.956

Gnomad EAS exome

AF:

0.881

Gnomad SAS exome

AF:

0.854

Gnomad FIN exome

AF:

0.957

Gnomad NFE exome

AF:

0.971

Gnomad OTH exome

AF:

0.928

GnomAD4 exome

AF:

0.947

AC:

1383934

AN:

1461790

Hom.:

661244

Cov.:

AF XY:

0.946

AC XY:

687652

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.413

Gnomad4 AMR exome

AF:

0.877

Gnomad4 ASJ exome

AF:

0.955

Gnomad4 EAS exome

AF:

0.910

Gnomad4 SAS exome

AF:

0.858

Gnomad4 FIN exome

AF:

0.957

Gnomad4 NFE exome

AF:

0.975

Gnomad4 OTH exome

AF:

0.920

GnomAD4 genome

AF:

0.806

AC:

122654

AN:

152228

Hom.:

53563

Cov.:

AF XY:

0.809

AC XY:

60233

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.435

Gnomad4 AMR

AF:

0.872

Gnomad4 ASJ

AF:

0.959

Gnomad4 EAS

AF:

0.887

Gnomad4 SAS

AF:

0.845

Gnomad4 FIN

AF:

0.955

Gnomad4 NFE

AF:

0.973

Gnomad4 OTH

AF:

0.845

Alfa

AF:

0.944

Hom.:

123922

Bravo

AF:

0.784

Asia WGS

AF:

0.831

AC:

2892

AN:

3478

EpiCase

AF:

0.969

EpiControl

AF:

0.969

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

CNBP-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 31, 2019

- -

Myotonic dystrophy type 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

Cadd

Benign

Dann

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: 1

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