Variant chr15-69417347-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001367805.3(KIF23):c.82-36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.956 in 1,516,826 control chromosomes in the GnomAD database, including 697,255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.88 ( 60256 hom., cov: 31)

Exomes 𝑓: 0.96 ( 636999 hom. )

Consequence

KIF23
NM_001367805.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.386

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 15-69417347-G-A is Benign according to our data. Variant chr15-69417347-G-A is described in ClinVar as [Benign]. Clinvar id is 1274067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 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.82-36G>A		intron_variant		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.82-36G>A		intron_variant			NM_001367805.3	ENSP00000504770	A2

Frequencies

GnomAD3 genomes

AF:

0.881

AC:

133927

AN:

152080

Hom.:

60247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.682

Gnomad AMI

AF:

0.976

Gnomad AMR

AF:

0.879

Gnomad ASJ

AF:

0.974

Gnomad EAS

AF:

0.822

Gnomad SAS

AF:

0.972

Gnomad FIN

AF:

0.956

Gnomad MID

AF:

0.934

Gnomad NFE

AF:

0.981

Gnomad OTH

AF:

0.906

GnomAD3 exomes

AF:

0.927

AC:

183956

AN:

198430

Hom.:

86194

AF XY:

0.939

AC XY:

101919

AN XY:

108538

show subpopulations

Gnomad AFR exome

AF:

0.671

Gnomad AMR exome

AF:

0.828

Gnomad ASJ exome

AF:

0.974

Gnomad EAS exome

AF:

0.809

Gnomad SAS exome

AF:

0.974

Gnomad FIN exome

AF:

0.959

Gnomad NFE exome

AF:

0.981

Gnomad OTH exome

AF:

0.954

GnomAD4 exome

AF:

0.964

AC:

1316153

AN:

1364628

Hom.:

636999

Cov.:

AF XY:

0.966

AC XY:

651190

AN XY:

674204

show subpopulations

Gnomad4 AFR exome

AF:

0.677

Gnomad4 AMR exome

AF:

0.841

Gnomad4 ASJ exome

AF:

0.975

Gnomad4 EAS exome

AF:

0.808

Gnomad4 SAS exome

AF:

0.975

Gnomad4 FIN exome

AF:

0.960

Gnomad4 NFE exome

AF:

0.982

Gnomad4 OTH exome

AF:

0.949

GnomAD4 genome

AF:

0.880

AC:

133971

AN:

152198

Hom.:

60256

Cov.:

AF XY:

0.879

AC XY:

65405

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.682

Gnomad4 AMR

AF:

0.879

Gnomad4 ASJ

AF:

0.974

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.972

Gnomad4 FIN

AF:

0.956

Gnomad4 NFE

AF:

0.981

Gnomad4 OTH

AF:

0.906

Alfa

AF:

0.898

Hom.:

10498

Bravo

AF:

0.866

Asia WGS

AF:

0.887

AC:

3084

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.1

DANN

Benign

0.59

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