rs10972040

Positions:

• chr9-34292857-T-C

Variant summary

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

The NM_194313.4(KIF24):​c.912-2468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,180 control chromosomes in the GnomAD database, including 1,517 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 0.12 (1517 hom., cov: 32)
• Consequence: KIF24 NM_194313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF24	NM_194313.4	c.912-2468A>G		intron_variant		ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7	c.912-2468A>G		intron_variant		5	NM_194313.4	ENSP00000384433	P1
KIF24	ENST00000379174.7	c.813+13395A>G		intron_variant		5		ENSP00000368472

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18755 AN: 152062 Hom.: 1517 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.123 AC: 18744 AN: 152180 Hom.: 1517 Cov.: 32 AF XY: 0.120 AC XY: 8912 AN XY: 74402

Gnomad4 AFR AF: 0.0333

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.0620

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.127

Alfa AF: 0.144 Hom.: 228

Bravo AF: 0.116

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.63

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: rs10972040; hg19: chr9-34292855; COSMIC: COSV61453881;