Genetic Variant NM_194313.4:c.3258G>A (chr9-34256349-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

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

Publications

19 publications found

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 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

KIF24 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.055).

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 rank	MANE	Protein	UniProt
KIF24	NM_194313.4 link	c.3258G>A	p.Gly1086Gly	synonymous_variant	Exon 11 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.3258G>A	p.Gly1086Gly	synonymous_variant	Exon 11 of 13	5	NM_194313.4	ENSP00000384433.1		Q5T7B8-1
KIF24	ENST00000379174.7 link	c.2856G>A	p.Gly952Gly	synonymous_variant	Exon 7 of 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

GnomAD2 exomes

AF:

0.404

AC:

99788

AN:

246818

AF XY:

0.405

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 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

African (AFR)

AF:

0.280

AC:

9365

AN:

33480

American (AMR)

AF:

0.472

AC:

21072

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.351

AC:

9164

AN:

26120

East Asian (EAS)

AF:

0.688

AC:

27298

AN:

39690

South Asian (SAS)

AF:

0.499

AC:

42996

AN:

86244

European-Finnish (FIN)

AF:

0.338

AC:

17947

AN:

53152

Middle Eastern (MID)

AF:

0.418

AC:

2408

AN:

5766

European-Non Finnish (NFE)

AF:

0.334

AC:

371532

AN:

1111702

Other (OTH)

AF:

0.371

AC:

22395

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

20019

40039

60058

80078

100097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12262

24524

36786

49048

61310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.346

AC:

52602

AN:

151992

Hom.:

9871

Cov.:

AF XY:

0.354

AC XY:

26327

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.272

AC:

11292

AN:

41492

American (AMR)

AF:

0.401

AC:

6112

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1189

AN:

3472

East Asian (EAS)

AF:

0.726

AC:

3750

AN:

5166

South Asian (SAS)

AF:

0.529

AC:

2542

AN:

4808

European-Finnish (FIN)

AF:

0.344

AC:

3635

AN:

10570

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.337

AC:

22860

AN:

67914

Other (OTH)

AF:

0.371

AC:

784

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1707

3414

5120

6827

8534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.340

Hom.:

21882

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

(source)

DANN

Benign

0.53

PhyloP100

0.62

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over