Menu
GeneBe

9-128166251-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001131016.2(CIZ1):c.2643G>A(p.Thr881=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,470,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000062 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000079 ( 0 hom. )

Consequence

CIZ1
NM_001131016.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.04
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 9-128166251-C-T is Benign according to our data. Variant chr9-128166251-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2851915.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.04 with no splicing effect.
BS2
High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CIZ1NM_001131016.2 linkuse as main transcriptc.2643G>A p.Thr881= synonymous_variant 17/17 ENST00000372938.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CIZ1ENST00000372938.10 linkuse as main transcriptc.2643G>A p.Thr881= synonymous_variant 17/171 NM_001131016.2 P2Q9ULV3-1

Frequencies

GnomAD3 genomes
AF:
0.0000620
AC:
9
AN:
145210
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000252
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000683
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000106
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000607
AC:
1
AN:
164676
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
86648
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000146
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000785
AC:
104
AN:
1324836
Hom.:
0
Cov.:
33
AF XY:
0.0000663
AC XY:
43
AN XY:
648338
show subpopulations
Gnomad4 AFR exome
AF:
0.0000328
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000972
Gnomad4 OTH exome
AF:
0.0000565
GnomAD4 genome
AF:
0.0000620
AC:
9
AN:
145210
Hom.:
0
Cov.:
31
AF XY:
0.0000283
AC XY:
2
AN XY:
70604
show subpopulations
Gnomad4 AFR
AF:
0.0000252
Gnomad4 AMR
AF:
0.0000683
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000106
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000323
Hom.:
0
Bravo
AF:
0.0000756

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Dystonic disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeNov 17, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
6.4
DANN
Benign
0.88
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs773659289; hg19: chr9-130928530; API