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GeneBe

9-128166332-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001131016.2(CIZ1):c.2562C>T(p.Asn854=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 in 1,565,736 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00055 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 3 hom. )

Consequence

CIZ1
NM_001131016.2 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.717
Variant links:
Genes affected
CIZ1 (HGNC:16744): (CDKN1A interacting zinc finger protein 1) The protein encoded by this gene is a zinc finger DNA binding protein that interacts with CIP1, part of a complex with cyclin E. The encoded protein may regulate the cellular localization of CIP1. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-128166332-G-A is Benign according to our data. Variant chr9-128166332-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 695540.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128166332-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-0.717 with no splicing effect.
BS2
High AC in GnomAd4 at 83 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CIZ1NM_001131016.2 linkuse as main transcriptc.2562C>T p.Asn854= synonymous_variant 17/17 ENST00000372938.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CIZ1ENST00000372938.10 linkuse as main transcriptc.2562C>T p.Asn854= synonymous_variant 17/171 NM_001131016.2 P2Q9ULV3-1

Frequencies

GnomAD3 genomes
AF:
0.000546
AC:
83
AN:
152142
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000660
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000956
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000412
AC:
71
AN:
172238
Hom.:
0
AF XY:
0.000339
AC XY:
31
AN XY:
91480
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000384
Gnomad ASJ exome
AF:
0.00116
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000436
Gnomad NFE exome
AF:
0.000703
Gnomad OTH exome
AF:
0.000850
GnomAD4 exome
AF:
0.000381
AC:
538
AN:
1413594
Hom.:
3
Cov.:
33
AF XY:
0.000405
AC XY:
283
AN XY:
698412
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000539
Gnomad4 ASJ exome
AF:
0.00115
Gnomad4 EAS exome
AF:
0.0000268
Gnomad4 SAS exome
AF:
0.0000125
Gnomad4 FIN exome
AF:
0.000736
Gnomad4 NFE exome
AF:
0.000412
Gnomad4 OTH exome
AF:
0.000341
GnomAD4 genome
AF:
0.000546
AC:
83
AN:
152142
Hom.:
0
Cov.:
32
AF XY:
0.000484
AC XY:
36
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000660
Gnomad4 NFE
AF:
0.000956
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000900
Hom.:
0
Bravo
AF:
0.000287

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Likely benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2021- -
Likely benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
CIZ1-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesDec 03, 2019This 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). -
Dystonic disorder Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 29, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
5.8
DANN
Benign
0.92
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs11549264; hg19: chr9-130928611; API