9-128166332-G-A

Variant names:

• chr9-128166332-G-A
• rs11549264
• NM_001131016.2:c.2562C>T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_001131016.2(CIZ1):​c.2562C>T​(p.Asn854Asn) 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
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.717

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CIZ1	NM_001131016.2	c.2562C>T	p.Asn854Asn	synonymous_variant	Exon 17 of 17	ENST00000372938.10	NP_001124488.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIZ1	ENST00000372938.10	c.2562C>T	p.Asn854Asn	synonymous_variant	Exon 17 of 17	1	NM_001131016.2	ENSP00000362029.5

Frequencies

GnomAD3 genomes AF: 0.000546 AC: 83 AN: 152142 Hom.: 0 Cov.: 32

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

GnomAD2 exomes AF: 0.000412 AC: 71 AN: 172238 AF XY: 0.000339

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 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

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 32456

Gnomad4 AMR exome AF: 0.0000539 AC: 2 AN: 37132

Gnomad4 ASJ exome AF: 0.00115 AC: 29 AN: 25262

Gnomad4 EAS exome AF: 0.0000268 AC: 1 AN: 37252

Gnomad4 SAS exome AF: 0.0000125 AC: 1 AN: 80256

Gnomad4 FIN exome AF: 0.000736 AC: 37 AN: 50302

Gnomad4 NFE exome AF: 0.000412 AC: 448 AN: 1086718

Gnomad4 Remaining exome AF: 0.000341 AC: 20 AN: 58584

GnomAD4 genome AF: 0.000546 AC: 83 AN: 152142 Hom.: 0 Cov.: 32 AF XY: 0.000484 AC XY: 36 AN XY: 74328

Gnomad4 AFR AF: 0.0000241 AC: 0.0000241371 AN: 0.0000241371

Gnomad4 AMR AF: 0.000262 AC: 0.000261814 AN: 0.000261814

Gnomad4 ASJ AF: 0.00173 AC: 0.00172911 AN: 0.00172911

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00 AC: 0 AN: 0

Gnomad4 FIN AF: 0.000660 AC: 0.000659755 AN: 0.000659755

Gnomad4 NFE AF: 0.000956 AC: 0.000955517 AN: 0.000955517

Gnomad4 OTH AF: 0.00 AC: 0 AN: 0

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

Submissions by phenotype

not provided Benign:3

Apr 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

CIZ1-related disorder Benign:1

Dec 03, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This 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

Oct 17, 2024

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	-0.79
CADD	Benign	5.8
DANN	Benign	0.92
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=99/1	polymorphism

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

Other links and lift over

dbSNP: rs11549264; hg19: chr9-130928611;