Variant chr15-69417409-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001367805.3(KIF23):c.108C>A(p.Gly36=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0372 in 1,612,196 control chromosomes in the GnomAD database, including 3,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.084 ( 989 hom., cov: 32)

Exomes 𝑓: 0.032 ( 2297 hom. )

Consequence

KIF23
NM_001367805.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.629

Variant links:

Genes affected

KIF23 (HGNC:6392): (kinesin family member 23) The protein encoded by this gene is a member of kinesin-like protein family. This family includes microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. This protein has been shown to cross-bridge antiparallel microtubules and drive microtubule movement in vitro. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2013]

KIF23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BP6

Variant 15-69417409-C-A is Benign according to our data. Variant chr15-69417409-C-A is described in ClinVar as [Benign]. Clinvar id is 1182474.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.629 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF23	NM_001367805.3 linkuse as main transcript	c.108C>A	p.Gly36=	synonymous_variant	3/24	ENST00000679126.1	NP_001354734.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF23	ENST00000679126.1 linkuse as main transcript	c.108C>A	p.Gly36=	synonymous_variant	3/24		NM_001367805.3	ENSP00000504770	A2

Frequencies

GnomAD3 genomes

AF:

0.0837

AC:

12730

AN:

152084

Hom.:

985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.0433

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0189

Gnomad OTH

AF:

0.0698

GnomAD3 exomes

AF:

0.0633

AC:

15797

AN:

249670

Hom.:

1178

AF XY:

0.0541

AC XY:

7299

AN XY:

135014

show subpopulations

Gnomad AFR exome

AF:

0.201

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.00657

Gnomad EAS exome

AF:

0.186

Gnomad SAS exome

AF:

0.0210

Gnomad FIN exome

AF:

0.0407

Gnomad NFE exome

AF:

0.0181

Gnomad OTH exome

AF:

0.0410

GnomAD4 exome

AF:

0.0323

AC:

47217

AN:

1459994

Hom.:

2297

Cov.:

AF XY:

0.0309

AC XY:

22409

AN XY:

726302

show subpopulations

Gnomad4 AFR exome

AF:

0.192

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.00617

Gnomad4 EAS exome

AF:

0.191

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.0401

Gnomad4 NFE exome

AF:

0.0181

Gnomad4 OTH exome

AF:

0.0398

GnomAD4 genome

AF:

0.0838

AC:

12756

AN:

152202

Hom.:

989

Cov.:

AF XY:

0.0853

AC XY:

6347

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.195

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.178

Gnomad4 SAS

AF:

0.0243

Gnomad4 FIN

AF:

0.0433

Gnomad4 NFE

AF:

0.0189

Gnomad4 OTH

AF:

0.0695

Alfa

AF:

0.0330

Hom.:

321

Bravo

AF:

0.0946

Asia WGS

AF:

0.0950

AC:

331

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

9.0

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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