NM_012127.3:c.-5-1505dupT

Variant names:

• chr9-128192366-C-CA
• rs57931082
• ENST00000866501.1:c.-518dupT

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
• Publications: 0 publications found

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]

DNM1 Gene-Disease associations (from GenCC):

• genetic developmental and epileptic encephalopathy

  Inheritance: AR, AD Classification: DEFINITIVE, MODERATE Submitted by: ClinGen
• developmental and epileptic encephalopathy, 31A

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• developmental and epileptic encephalopathy, 31B

  Inheritance: AR, AD Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• Lennox-Gastaut syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012127.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIZ1	NM_012127.3		c.-5-1505dupT		intron	N/A	NP_036259.2
	CIZ1	NM_001131015.2		c.-5-1505dupT		intron	N/A	NP_001124487.1	Q9ULV3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIZ1	ENST00000866501.1		c.-518dupT		5_prime_UTR	Exon 1 of 17	ENSP00000536560.1
	CIZ1	ENST00000866502.1		c.-641dupT		5_prime_UTR	Exon 1 of 16	ENSP00000536561.1
	CIZ1	ENST00000866503.1		c.-518dupT		5_prime_UTR	Exon 1 of 16	ENSP00000536562.1

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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

Other links and lift over

dbSNP: rs57931082; hg19: chr9-130954645;