chr9-34284946-G-A

Variant names:

• chr9-34284946-G-A
• rs17350373
• NM_194313.4:c.1215+1671C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.75).
• 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 rank	MANE	Protein	UniProt
KIF24	NM_194313.4	c.1215+1671C>T		intron_variant	Intron 6 of 12	ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7	c.1215+1671C>T		intron_variant	Intron 6 of 12	5	NM_194313.4	ENSP00000384433.1
KIF24	ENST00000379174.7	c.814-13016C>T		intron_variant	Intron 2 of 8	5		ENSP00000368472.3

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

African (AFR) AF: 0.140 AC: 5800 AN: 41490

American (AMR) AF: 0.353 AC: 5394 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1831 AN: 5170

South Asian (SAS) AF: 0.576 AC: 2770 AN: 4806

European-Finnish (FIN) AF: 0.388 AC: 4093 AN: 10542

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30708 AN: 67960

Other (OTH) AF: 0.385 AC: 811 AN: 2106

Alfa AF: 0.423 Hom.: 15446

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
PhyloP100		-0.079
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: rs17350373; hg19: chr9-34284944;