rs10972055

Positions:

• chr9-34318656-G-A

Variant summary

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

The NM_194313.4(KIF24):​c.-25-7285C>T variant causes a intron change. The variant allele was found at a frequency of 0.584 in 1,520,396 control chromosomes in the GnomAD database, including 271,264 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 0.47 (20117 hom., cov: 34)
  • Exomes 𝑓: 0.60 (251147 hom.)
• Consequence: KIF24 NM_194313.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.01

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]

SERPINH1P1 (HGNC:19917): (serpin family H member 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• 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/exons	MANE	Protein	UniProt
KIF24	NM_194313.4	c.-25-7285C>T		intron_variant		ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7	c.-25-7285C>T		intron_variant		5	NM_194313.4	ENSP00000384433	P1
SERPINH1P1	ENST00000419794.1	n.250G>A		non_coding_transcript_exon_variant	1/1
KIF24	ENST00000684219.1	c.-26+784C>T		intron_variant				ENSP00000506725

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72176 AN: 152084 Hom.: 20118 Cov.: 34

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.596 AC: 816035 AN: 1368194 Hom.: 251147 Cov.: 30 AF XY: 0.600 AC XY: 408787 AN XY: 681754

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.473

Gnomad4 ASJ exome AF: 0.590

Gnomad4 EAS exome AF: 0.304

Gnomad4 SAS exome AF: 0.633

Gnomad4 FIN exome AF: 0.578

Gnomad4 NFE exome AF: 0.626

Gnomad4 OTH exome AF: 0.566

GnomAD4 genome AF: 0.474 AC: 72178 AN: 152202 Hom.: 20117 Cov.: 34 AF XY: 0.473 AC XY: 35218 AN XY: 74410

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.512

Alfa AF: 0.550 Hom.: 3101

Bravo AF: 0.451

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	15
DANN	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10972055; hg19: chr9-34318654;