Variant 20-21126073-C-CG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PVS1_StrongBP6_ModerateBA1

The NM_001276389.2(KIZ):c.39dupG(p.Pro14fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 1,459,588 control chromosomes in the GnomAD database, including 276,322 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 23597 hom., cov: 0)

Exomes 𝑓: 0.62 ( 252725 hom. )

Consequence

KIZ
NM_001276389.2 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.62

Variant links:

Genes affected

KIZ (HGNC:15865): (kizuna centrosomal protein) The protein encoded by this gene localizes to centrosomes, strengthening and stabilizing the pericentriolar region prior to spindle formation. The encoded protein usually remains with the mother centrosome after centrosomal duplication. Sevral transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]

KIZ links:

KIZ (HGNC:):

KIZ links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.979 CDS is truncated, and there are 2 pathogenic variants in the truncated region.

BP6

Variant 20-21126073-C-CG is Benign according to our data. Variant chr20-21126073-C-CG is described in ClinVar as [Benign]. Clinvar id is 3028538.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIZ	NM_018474.6 linkuse as main transcript	c.-43_-42insG		upstream_gene_variant		ENST00000619189.5	NP_060944.3	Q2M2Z5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIZ	ENST00000619189.5 linkuse as main transcript	c.-43_-42insG		upstream_gene_variant		1	NM_018474.6	ENSP00000479542.1		Q2M2Z5-1

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81667

AN:

152008

Hom.:

23591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.516

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.696

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.731

Gnomad FIN

AF:

0.674

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.607

GnomAD3 exomes

AF:

0.602

AC:

44672

AN:

74190

Hom.:

13937

AF XY:

0.622

AC XY:

26238

AN XY:

42208

show subpopulations

Gnomad AFR exome

AF:

0.266

Gnomad AMR exome

AF:

0.456

Gnomad ASJ exome

AF:

0.681

Gnomad EAS exome

AF:

0.513

Gnomad SAS exome

AF:

0.715

Gnomad FIN exome

AF:

0.654

Gnomad NFE exome

AF:

0.608

Gnomad OTH exome

AF:

0.611

GnomAD4 exome

AF:

0.618

AC:

807360

AN:

1307462

Hom.:

252725

Cov.:

AF XY:

0.623

AC XY:

399671

AN XY:

641734

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.485

Gnomad4 ASJ exome

AF:

0.686

Gnomad4 EAS exome

AF:

0.509

Gnomad4 SAS exome

AF:

0.724

Gnomad4 FIN exome

AF:

0.657

Gnomad4 NFE exome

AF:

0.621

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.537

AC:

81712

AN:

152126

Hom.:

23597

Cov.:

AF XY:

0.544

AC XY:

40461

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.310

Gnomad4 AMR

AF:

0.549

Gnomad4 ASJ

AF:

0.696

Gnomad4 EAS

AF:

0.547

Gnomad4 SAS

AF:

0.731

Gnomad4 FIN

AF:

0.674

Gnomad4 NFE

AF:

0.627

Gnomad4 OTH

AF:

0.607

Alfa

AF:

0.572

Hom.:

3149

Bravo

AF:

0.514

Asia WGS

AF:

0.614

AC:

2136

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Retinal dystrophy

Benign:1

Benign, criteria provided, single submitter

research

Dept Of Ophthalmology, Nagoya University

Oct 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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