rs17350373

Positions:

• chr9-34284946-G-A

Variant summary

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

The NM_194313.4(KIF24):​c.1215+1671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,012 control chromosomes in the GnomAD database, including 10,858 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 (10858 hom., cov: 31)
• Consequence: KIF24 NM_194313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF24	NM_194313.4	c.1215+1671C>T		intron_variant		ENST00000402558.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF24	ENST00000402558.7	c.1215+1671C>T		intron_variant		5	NM_194313.4	P1
KIF24	ENST00000379174.7	c.814-13016C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53455 AN: 151894 Hom.: 10853 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.383

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.352 AC: 53467 AN: 152012 Hom.: 10858 Cov.: 31 AF XY: 0.354 AC XY: 26313 AN XY: 74294

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.385

Alfa AF: 0.428 Hom.: 12790

Bravo AF: 0.336

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.6
DANN	Benign	0.84

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: rs17350373; hg19: chr9-34284944;