dbSNP rs17258783: KIF24:c.*1281G>A (chr9-34253099-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_194313.4(KIF24):c.*1281G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,536 control chromosomes in the GnomAD database, including 2,325 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 0.16 ( 2321 hom., cov: 32)

Exomes 𝑓: 0.16 ( 4 hom. )

Consequence

KIF24
NM_194313.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46

Publications

11 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF24	NM_194313.4 link	c.*1281G>A		3_prime_UTR_variant	Exon 13 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.*1281G>A		3_prime_UTR_variant	Exon 13 of 13	5	NM_194313.4	ENSP00000384433.1		Q5T7B8-1
KIF24	ENST00000379174.7 link	c.*1281G>A		3_prime_UTR_variant	Exon 9 of 9	5		ENSP00000368472.3		Q5T7B8-2

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24068

AN:

152000

Hom.:

2318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.162

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.0533

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.156

AC:

AN:

418

Hom.:

Cov.:

AF XY:

0.164

AC XY:

AN XY:

226

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.208

AC:

AN:

120

Middle Eastern (MID)

AF:

0.0455

AC:

AN:

110

European-Non Finnish (NFE)

AF:

0.184

AC:

AN:

Other (OTH)

AF:

0.233

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.158

AC:

24071

AN:

152118

Hom.:

2321

Cov.:

AF XY:

0.159

AC XY:

11813

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0684

AC:

2839

AN:

41530

American (AMR)

AF:

0.162

AC:

2472

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

499

AN:

3466

East Asian (EAS)

AF:

0.0536

AC:

277

AN:

5164

South Asian (SAS)

AF:

0.245

AC:

1183

AN:

4822

European-Finnish (FIN)

AF:

0.187

AC:

1973

AN:

10550

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14241

AN:

67984

Other (OTH)

AF:

0.165

AC:

350

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1020

2041

3061

4082

5102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.186

Hom.:

7784

Bravo

AF:

0.149

Asia WGS

AF:

0.150

AC:

522

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

1.5

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