chr9-34253490-A-G

Variant names:

• chr9-34253490-A-G
• rs4574933
• NM_194313.4:c.*890T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194313.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF24	NM_194313.4	MANE Select	c.*890T>C		3_prime_UTR	Exon 13 of 13	NP_919289.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF24	ENST00000402558.7	TSL:5 MANE Select	c.*890T>C		3_prime_UTR	Exon 13 of 13	ENSP00000384433.1
	KIF24	ENST00000379174.7	TSL:5	c.*890T>C		3_prime_UTR	Exon 9 of 9	ENSP00000368472.3

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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.242 AC: 16 AN: 66

Other (OTH) AF: 0.00 AC: 0 AN: 10

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

African (AFR) AF: 0.0684 AC: 2841 AN: 41534

American (AMR) AF: 0.163 AC: 2487 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.0540 AC: 280 AN: 5182

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4828

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14345 AN: 67978

Other (OTH) AF: 0.168 AC: 355 AN: 2116

Alfa AF: 0.189 Hom.: 3719

Bravo AF: 0.150

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.0070
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: rs4574933; hg19: chr9-34253488;