rs10972030

Variant names:

• chr9-34266325-T-C
• rs10972030
• NM_194313.4:c.1443+2932A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194313.4(KIF24):​c.1443+2932A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,030 control chromosomes in the GnomAD database, including 20,131 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 0.48 (20131 hom., cov: 32)
• Consequence: KIF24 NM_194313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 5 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF24	NM_194313.4	c.1443+2932A>G		intron_variant	Intron 8 of 12	ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7	c.1443+2932A>G		intron_variant	Intron 8 of 12	5	NM_194313.4	ENSP00000384433.1
KIF24	ENST00000379174.7	c.1041+2932A>G		intron_variant	Intron 4 of 8	5		ENSP00000368472.3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72249 AN: 151912 Hom.: 20132 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.475 AC: 72250 AN: 152030 Hom.: 20131 Cov.: 32 AF XY: 0.474 AC XY: 35213 AN XY: 74284

African (AFR) AF: 0.173 AC: 7195 AN: 41502

American (AMR) AF: 0.486 AC: 7410 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1858 AN: 5164

South Asian (SAS) AF: 0.639 AC: 3067 AN: 4796

European-Finnish (FIN) AF: 0.561 AC: 5913 AN: 10538

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42882 AN: 67982

Other (OTH) AF: 0.514 AC: 1085 AN: 2112

Alfa AF: 0.553 Hom.: 8260

Bravo AF: 0.452

Asia WGS AF: 0.488 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10972030; hg19: chr9-34266323; COSMIC: COSV61453825;