9-128192366-CAAAAA-CAAAAAAAA

Variant names:

• chr9-128192366-C-CAAA
• rs57931082
• NM_012127.3:c.-5-1507_-5-1505dupTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_012127.3(CIZ1):​c.-5-1507_-5-1505dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00050 (0 hom., cov: 0)
• Consequence: CIZ1 NM_012127.3 intron
• Clinical Significance: Not reported in ClinVar
• 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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 70 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIZ1	NM_012127.3	c.-5-1507_-5-1505dupTTT		intron_variant	Intron 1 of 16		NP_036259.2
CIZ1	NM_001131015.2	c.-5-1507_-5-1505dupTTT		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_-5-1504insTTT		intron_variant	Intron 4 of 19	5		ENSP00000489425.1
CIZ1	ENST00000372948.7	c.-5-1505_-5-1504insTTT		intron_variant	Intron 1 of 17	2		ENSP00000362039.3
CIZ1	ENST00000651955.1	c.-5-1505_-5-1504insTTT		intron_variant	Intron 2 of 19			ENSP00000498625.1

Frequencies

GnomAD3 genomes AF: 0.000502 AC: 70 AN: 139490 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000285

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000268

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000123

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000502 AC: 70 AN: 139506 Hom.: 0 Cov.: 0 AF XY: 0.000551 AC XY: 37 AN XY: 67178

Gnomad4 AFR AF: 0.00149

Gnomad4 AMR AF: 0.000285

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000268

Gnomad4 NFE AF: 0.000123

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57931082; hg19: chr9-130954645;