rs1384313

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000422453.7(CNBP):​c.-14-5460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,224 control chromosomes in the GnomAD database, including 61,419 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.89 ( 61419 hom., cov: 32)

Consequence

CNBP
ENST00000422453.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CNBPNM_003418.5 linkuse as main transcriptc.-14-5460G>A intron_variant ENST00000422453.7 NP_003409.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CNBPENST00000422453.7 linkuse as main transcriptc.-14-5460G>A intron_variant 1 NM_003418.5 ENSP00000410619 P62633-1

Frequencies

GnomAD3 genomes
AF:
0.893
AC:
135797
AN:
152106
Hom.:
61410
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.732
Gnomad AMI
AF:
0.997
Gnomad AMR
AF:
0.913
Gnomad ASJ
AF:
0.965
Gnomad EAS
AF:
0.887
Gnomad SAS
AF:
0.847
Gnomad FIN
AF:
0.954
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.974
Gnomad OTH
AF:
0.911
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.892
AC:
135843
AN:
152224
Hom.:
61419
Cov.:
32
AF XY:
0.891
AC XY:
66305
AN XY:
74428
show subpopulations
Gnomad4 AFR
AF:
0.732
Gnomad4 AMR
AF:
0.913
Gnomad4 ASJ
AF:
0.965
Gnomad4 EAS
AF:
0.887
Gnomad4 SAS
AF:
0.847
Gnomad4 FIN
AF:
0.954
Gnomad4 NFE
AF:
0.974
Gnomad4 OTH
AF:
0.907
Alfa
AF:
0.948
Hom.:
37041
Bravo
AF:
0.883
Asia WGS
AF:
0.848
AC:
2950
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.46
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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.

Other links and lift over

dbSNP: rs1384313; hg19: chr3-128896074; API