dbSNP rs17350674: KIF24:p.Trp218Leu (chr9-34306412-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_194313.4(KIF24):c.653G>T(p.Trp218Leu) variant causes a missense change. The variant allele was found at a frequency of 0.174 in 1,607,156 control chromosomes in the GnomAD database, including 27,155 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1924 hom., cov: 32)

Exomes 𝑓: 0.18 ( 25231 hom. )

Consequence

KIF24
NM_194313.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.68

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016726851).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF24	NM_194313.4 link	c.653G>T	p.Trp218Leu	missense_variant	Exon 3 of 13	ENST00000402558.7	NP_919289.2	Q5T7B8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7 link	c.653G>T	p.Trp218Leu	missense_variant	Exon 3 of 13	5	NM_194313.4	ENSP00000384433.1		Q5T7B8-1
KIF24	ENST00000379174.7 link	c.653G>T	p.Trp218Leu	missense_variant	Exon 2 of 9	5		ENSP00000368472.3		Q5T7B8-2

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20886

AN:

152062

Hom.:

1921

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0337

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.00481

Gnomad SAS

AF:

0.0960

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.152

GnomAD3 exomes

AF:

0.159

AC:

38722

AN:

244074

Hom.:

3699

AF XY:

0.162

AC XY:

21433

AN XY:

132468

show subpopulations

Gnomad AFR exome

AF:

0.0287

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.235

Gnomad EAS exome

AF:

0.00211

Gnomad SAS exome

AF:

0.111

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.204

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.178

AC:

258988

AN:

1454976

Hom.:

25231

Cov.:

AF XY:

0.177

AC XY:

128490

AN XY:

723922

show subpopulations

Gnomad4 AFR exome

AF:

0.0266

Gnomad4 AMR exome

AF:

0.128

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.00159

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.137

AC:

20890

AN:

152180

Hom.:

1924

Cov.:

AF XY:

0.137

AC XY:

10158

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0336

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.00482

Gnomad4 SAS

AF:

0.0955

Gnomad4 FIN

AF:

0.226

Gnomad4 NFE

AF:

0.194

Gnomad4 OTH

AF:

0.152

Alfa

AF:

0.178

Hom.:

4822

Bravo

AF:

0.130

TwinsUK

AF:

0.190

AC:

706

ALSPAC

AF:

0.181

AC:

696

ESP6500AA

AF:

0.0332

AC:

120

ESP6500EA

AF:

0.192

AC:

1565

ExAC

AF:

0.159

AC:

19144

Asia WGS

AF:

0.0720

AC:

250

AN:

3478

EpiCase

AF:

0.195

EpiControl

AF:

0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.42

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.039

T;.

Eigen

Uncertain

0.55

Eigen_PC

Uncertain

0.58

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.90

D;D

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.97

L;L

PrimateAI

Uncertain

0.71

PROVEAN

Pathogenic

-6.6

D;D

REVEL

Benign

0.19

Sift

Uncertain

0.012

D;D

Sift4G

Benign

0.44

T;T

Polyphen

0.98

D;.

Vest4

0.23

ClinPred

0.041

GERP RS

5.6

Varity_R

0.52

gMVP

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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