rs10814083

Variant names:

• chr9-34256349-C-G
• rs10814083
• NM_194313.4:c.3258G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-34256349-C-G
• chr9-34256349-C-T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_194313.4(KIF24):​c.3258G>C​(p.Gly1086Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G1086G) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIF24 NM_194313.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620
• Publications: 19 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.066).
• BP7: Synonymous conserved (PhyloP=0.62 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF24	NM_194313.4	MANE Select	c.3258G>C	p.Gly1086Gly	synonymous	Exon 11 of 13	NP_919289.2	Q5T7B8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF24	ENST00000402558.7	TSL:5 MANE Select	c.3258G>C	p.Gly1086Gly	synonymous	Exon 11 of 13	ENSP00000384433.1	Q5T7B8-1
	KIF24	ENST00000911288.1		c.3042G>C	p.Gly1014Gly	synonymous	Exon 10 of 12	ENSP00000581347.1
	KIF24	ENST00000911291.1		c.3030G>C	p.Gly1010Gly	synonymous	Exon 9 of 11	ENSP00000581350.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 52

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.38
DANN	Benign	0.49
PhyloP100		0.62

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: rs10814083; hg19: chr9-34256347;