9-128192366-C-CA

Variant names:

• chr9-128192366-C-CA
• rs57931082
• NM_012127.3:c.-5-1505dupT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_012127.3(CIZ1):​c.-5-1505dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.96 (63732 hom., cov: 0)
• Consequence: CIZ1 NM_012127.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.202

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]

DNM1 (HGNC:2972): (dynamin 1) This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. More than sixty highly conserved copies of the 3' region of this gene are found elsewhere in the genome, particularly on chromosomes Y and 15. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 9-128192366-C-CA is Benign according to our data. Variant chr9-128192366-C-CA is described in ClinVar as [Benign]. Clinvar id is 1272244.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIZ1	NM_012127.3	c.-5-1505dupT		intron_variant	Intron 1 of 16		NP_036259.2
CIZ1	NM_001131015.2	c.-5-1505dupT		intron_variant	Intron 1 of 17		NP_001124487.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIZ1	ENST00000634901.1	c.-5-1505_-5-1504insT		intron_variant	Intron 4 of 19	5		ENSP00000489425.1
CIZ1	ENST00000372948.7	c.-5-1505_-5-1504insT		intron_variant	Intron 1 of 17	2		ENSP00000362039.3
CIZ1	ENST00000651955.1	c.-5-1505_-5-1504insT		intron_variant	Intron 2 of 19			ENSP00000498625.1

Frequencies

GnomAD3 genomes AF: 0.956 AC: 133306 AN: 139490 Hom.: 63728 Cov.: 0

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.916

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.946

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.956 AC: 133316 AN: 139506 Hom.: 63732 Cov.: 0 AF XY: 0.955 AC XY: 64132 AN XY: 67184

African (AFR) AF: 0.949 AC: 35636 AN: 37568

American (AMR) AF: 0.909 AC: 12776 AN: 14050

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 3273 AN: 3396

East Asian (EAS) AF: 0.984 AC: 4654 AN: 4732

South Asian (SAS) AF: 0.983 AC: 4150 AN: 4220

European-Finnish (FIN) AF: 0.965 AC: 7204 AN: 7466

Middle Eastern (MID) AF: 0.912 AC: 259 AN: 284

European-Non Finnish (NFE) AF: 0.967 AC: 62809 AN: 64980

Other (OTH) AF: 0.946 AC: 1812 AN: 1916

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 05, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs57931082; hg19: chr9-130954645;