Variant 9-34255990-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_194313.4(KIF24):c.3617T>G(p.Leu1206Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00924 in 1,613,834 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0058 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0096 ( 75 hom. )

Consequence

KIF24
NM_194313.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.129

Variant links:

Genes affected

KIF24 (HGNC:19916): (kinesin family member 24) This gene encodes a member of the kinesin superfamily of microtubule-based motor proteins which are involved in the intracellular transport of membranous organelles, protein complexes, and mRNAs. They also play critical roles in mitosis, morphogenesis, and signal transduction. The encoded protein contains an N-terminal sterile alpha motif (SAM) domain and an ATP-binding kinesin motor domain. It binds centriolar coiled coil protein 110 and centrosomal protein 97 and localizes to the mother centriole to regulate ciliogenesis by controlling microtubule polymerization. [provided by RefSeq, Mar 2017]

KIF24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0047819912).

BP6

Variant 9-34255990-A-C is Benign according to our data. Variant chr9-34255990-A-C is described in ClinVar as [Benign]. Clinvar id is 3024785.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF24	NM_194313.4 linkuse as main transcript	c.3617T>G	p.Leu1206Arg	missense_variant	11/13	ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7 linkuse as main transcript	c.3617T>G	p.Leu1206Arg	missense_variant	11/13	5	NM_194313.4	ENSP00000384433	P1	Q5T7B8-1
KIF24	ENST00000379174.7 linkuse as main transcript	c.3215T>G	p.Leu1072Arg	missense_variant	7/9	5		ENSP00000368472		Q5T7B8-2

Frequencies

GnomAD3 genomes

AF:

0.00581

AC:

883

AN:

152020

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00143

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00360

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00595

AC:

1494

AN:

251100

Hom.:

AF XY:

0.00599

AC XY:

813

AN XY:

135694

show subpopulations

Gnomad AFR exome

AF:

0.00172

Gnomad AMR exome

AF:

0.00295

Gnomad ASJ exome

AF:

0.00238

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.00324

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.00637

GnomAD4 exome

AF:

0.00960

AC:

14029

AN:

1461696

Hom.:

Cov.:

AF XY:

0.00929

AC XY:

6757

AN XY:

727130

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00297

Gnomad4 ASJ exome

AF:

0.00233

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000974

Gnomad4 FIN exome

AF:

0.00423

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.00774

GnomAD4 genome

AF:

0.00580

AC:

883

AN:

152138

Hom.:

Cov.:

AF XY:

0.00531

AC XY:

395

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.00142

Gnomad4 AMR

AF:

0.00360

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00816

Hom.:

Bravo

AF:

0.00551

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.0106

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.0102

AC:

ExAC

AF:

0.00651

AC:

790

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00823

EpiControl

AF:

0.0101

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

KIF24: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.42

CADD

Benign

6.4

DANN

Benign

0.97

DEOGEN2

Benign

0.0037

T;.

Eigen

Benign

-0.98

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.49

T;T

MetaRNN

Benign

0.0048

T;T

MetaSVM

Benign

-0.88

MutationAssessor

Uncertain

2.1

M;.

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.1

N;N

REVEL

Benign

0.083

Sift

Pathogenic

0.0

D;D

Sift4G

Benign

0.45

T;T

Polyphen

0.74

P;.

Vest4

0.089

MVP

0.67

ClinPred

0.0081

GERP RS

0.10

Varity_R

0.19

gMVP

0.24

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