rs4574933

Positions:

• chr9-34253490-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194313.4(KIF24):​c.*890T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,272 control chromosomes in the GnomAD database, including 2,348 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 (2347 hom., cov: 32)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: KIF24 NM_194313.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF24	NM_194313.4	c.*890T>C		3_prime_UTR_variant	13/13	ENST00000402558.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF24	ENST00000402558.7	c.*890T>C		3_prime_UTR_variant	13/13	5	NM_194313.4	P1
KIF24	ENST00000379174.7	c.*890T>C		3_prime_UTR_variant	9/9	5

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24216 AN: 152068 Hom.: 2344 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.209 AC: 18 AN: 86 Hom.: 1 Cov.: 0 AF XY: 0.197 AC XY: 13 AN XY: 66

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.159 AC: 24219 AN: 152186 Hom.: 2347 Cov.: 32 AF XY: 0.160 AC XY: 11882 AN XY: 74410

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.168

Alfa AF: 0.195 Hom.: 2946

Bravo AF: 0.150

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs4574933; hg19: chr9-34253488;