Variant 9-34256349-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_194313.4(KIF24):c.3258G>A(p.Gly1086Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,613,194 control chromosomes in the GnomAD database, including 108,833 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 9871 hom., cov: 32)

Exomes 𝑓: 0.36 ( 98962 hom. )

Consequence

KIF24
NM_194313.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.620

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=0.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF24	NM_194313.4 linkuse as main transcript	c.3258G>A	p.Gly1086Gly	synonymous_variant	11/13	ENST00000402558.7	NP_919289.2	Q5T7B8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7 linkuse as main transcript	c.3258G>A	p.Gly1086Gly	synonymous_variant	11/13	5	NM_194313.4	ENSP00000384433.1		Q5T7B8-1
KIF24	ENST00000379174.7 linkuse as main transcript	c.2856G>A	p.Gly952Gly	synonymous_variant	7/9	5		ENSP00000368472.3		Q5T7B8-2

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52554

AN:

151874

Hom.:

9857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.726

Gnomad SAS

AF:

0.527

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.366

GnomAD3 exomes

AF:

0.404

AC:

99788

AN:

246818

Hom.:

21937

AF XY:

0.405

AC XY:

54032

AN XY:

133506

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.484

Gnomad ASJ exome

AF:

0.350

Gnomad EAS exome

AF:

0.740

Gnomad SAS exome

AF:

0.502

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.334

Gnomad OTH exome

AF:

0.366

GnomAD4 exome

AF:

0.359

AC:

524177

AN:

1461202

Hom.:

98962

Cov.:

AF XY:

0.362

AC XY:

263189

AN XY:

726844

show subpopulations

Gnomad4 AFR exome

AF:

0.280

Gnomad4 AMR exome

AF:

0.472

Gnomad4 ASJ exome

AF:

0.351

Gnomad4 EAS exome

AF:

0.688

Gnomad4 SAS exome

AF:

0.499

Gnomad4 FIN exome

AF:

0.338

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.346

AC:

52602

AN:

151992

Hom.:

9871

Cov.:

AF XY:

0.354

AC XY:

26327

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.272

Gnomad4 AMR

AF:

0.401

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.726

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.337

Gnomad4 OTH

AF:

0.371

Alfa

AF:

0.340

Hom.:

14900

Bravo

AF:

0.347

Asia WGS

AF:

0.589

AC:

2042

AN:

3478

EpiCase

AF:

0.339

EpiControl

AF:

0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.47

DANN

Benign

0.53

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over