Variant chr20-21126163-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The ENST00000619189.5(KIZ):c.48C>T(p.Tyr16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,509,394 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0023 ( 12 hom. )

Consequence

KIZ
ENST00000619189.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.08

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 20-21126163-C-T is Benign according to our data. Variant chr20-21126163-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 778878.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-21126163-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=2.08 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIZ	NM_018474.6 linkuse as main transcript	c.48C>T	p.Tyr16=	synonymous_variant	1/13	ENST00000619189.5	NP_060944.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIZ	ENST00000619189.5 linkuse as main transcript	c.48C>T	p.Tyr16=	synonymous_variant	1/13	1	NM_018474.6	ENSP00000479542	P1	Q2M2Z5-1

Frequencies

GnomAD3 genomes

AF:

0.00194

AC:

295

AN:

152242

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000868

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.00656

Gnomad SAS

AF:

0.00289

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00201

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00233

AC:

263

AN:

113044

Hom.:

AF XY:

0.00232

AC XY:

144

AN XY:

61988

show subpopulations

Gnomad AFR exome

AF:

0.000340

Gnomad AMR exome

AF:

0.00112

Gnomad ASJ exome

AF:

0.00944

Gnomad EAS exome

AF:

0.00598

Gnomad SAS exome

AF:

0.00183

Gnomad FIN exome

AF:

0.000144

Gnomad NFE exome

AF:

0.00215

Gnomad OTH exome

AF:

0.00535

GnomAD4 exome

AF:

0.00226

AC:

3063

AN:

1357034

Hom.:

Cov.:

AF XY:

0.00226

AC XY:

1513

AN XY:

668450

show subpopulations

Gnomad4 AFR exome

AF:

0.000792

Gnomad4 AMR exome

AF:

0.00107

Gnomad4 ASJ exome

AF:

0.0118

Gnomad4 EAS exome

AF:

0.00556

Gnomad4 SAS exome

AF:

0.00249

Gnomad4 FIN exome

AF:

0.000278

Gnomad4 NFE exome

AF:

0.00199

Gnomad4 OTH exome

AF:

0.00399

GnomAD4 genome

AF:

0.00194

AC:

296

AN:

152360

Hom.:

Cov.:

AF XY:

0.00177

AC XY:

132

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.000866

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.00657

Gnomad4 SAS

AF:

0.00310

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.00201

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00293

Hom.:

Bravo

AF:

0.00212

Asia WGS

AF:

0.00606

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 23, 2024

- -

Retinal dystrophy

Benign:1

Likely 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

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Benign

0.86

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