chr9-34253099-C-T

Position:

• chr9-34253099-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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 -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/exons	MANE	UniProt
KIF24	NM_194313.4	c.*1281G>A		3_prime_UTR_variant	13/13	ENST00000402558.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF24	ENST00000402558.7	c.*1281G>A		3_prime_UTR_variant	13/13	5	NM_194313.4	P1
KIF24	ENST00000379174.7	c.*1281G>A		3_prime_UTR_variant	9/9	5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24068 AN: 152000 Hom.: 2318 Cov.: 32

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: 65 AN: 418 Hom.: 4 Cov.: 0 AF XY: 0.164 AC XY: 37 AN XY: 226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.184

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.158 AC: 24071 AN: 152118 Hom.: 2321 Cov.: 32 AF XY: 0.159 AC XY: 11813 AN XY: 74322

Gnomad4 AFR AF: 0.0684

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.165

Alfa AF: 0.195 Hom.: 5185

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	16
DANN	Benign	0.90

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: rs17258783; hg19: chr9-34253097;