Genetic Variant CIZ1:p.Pro409Pro (chr9-128178980-G-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001131016.2(CIZ1):c.1227C>A(p.Pro409Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00714 in 1,613,508 control chromosomes in the GnomAD database, including 394 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0079 ( 40 hom., cov: 33)

Exomes 𝑓: 0.0071 ( 354 hom. )

Consequence

CIZ1
NM_001131016.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -7.87

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]

CIZ1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 9-128178980-G-T is Benign according to our data. Variant chr9-128178980-G-T is described in ClinVar as [Benign]. Clinvar id is 413831.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-7.87 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIZ1	NM_001131016.2 link	c.1227C>A	p.Pro409Pro	synonymous_variant	Exon 8 of 17	ENST00000372938.10	NP_001124488.1	Q9ULV3-1A0A024R885

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIZ1	ENST00000372938.10 link	c.1227C>A	p.Pro409Pro	synonymous_variant	Exon 8 of 17	1	NM_001131016.2	ENSP00000362029.5		Q9ULV3-1

Frequencies

GnomAD3 genomes

AF:

0.00785

AC:

1190

AN:

151602

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000919

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.0848

Gnomad SAS

AF:

0.0372

Gnomad FIN

AF:

0.0400

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000987

Gnomad OTH

AF:

0.00912

GnomAD3 exomes

AF:

0.0154

AC:

3848

AN:

249704

Hom.:

109

AF XY:

0.0159

AC XY:

2148

AN XY:

135080

show subpopulations

Gnomad AFR exome

AF:

0.00129

Gnomad AMR exome

AF:

0.000145

Gnomad ASJ exome

AF:

0.00259

Gnomad EAS exome

AF:

0.0894

Gnomad SAS exome

AF:

0.0334

Gnomad FIN exome

AF:

0.0381

Gnomad NFE exome

AF:

0.00186

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.00706

AC:

10324

AN:

1461786

Hom.:

354

Cov.:

AF XY:

0.00775

AC XY:

5639

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.000478

Gnomad4 AMR exome

AF:

0.000224

Gnomad4 ASJ exome

AF:

0.00191

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.0309

Gnomad4 FIN exome

AF:

0.0360

Gnomad4 NFE exome

AF:

0.000701

Gnomad4 OTH exome

AF:

0.0106

GnomAD4 genome

AF:

0.00788

AC:

1195

AN:

151722

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

763

AN XY:

74162

show subpopulations

Gnomad4 AFR

AF:

0.00109

Gnomad4 AMR

AF:

0.000918

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.0850

Gnomad4 SAS

AF:

0.0375

Gnomad4 FIN

AF:

0.0400

Gnomad4 NFE

AF:

0.000988

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00186

Hom.:

Bravo

AF:

0.00452

EpiCase

AF:

0.000763

EpiControl

AF:

0.000889

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CIZ1-related disorder

Benign:1

May 16, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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). -

Dystonic disorder

Benign:1

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.55

DANN

Benign

0.28

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.

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