rs10972055

Variant names:

• chr9-34318656-G-A
• rs10972055
• NM_194313.4:c.-25-7285C>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.-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
• 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]

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIF24	NM_194313.4	c.-25-7285C>T		intron_variant	Intron 1 of 12	ENST00000402558.7	NP_919289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF24	ENST00000402558.7	c.-25-7285C>T		intron_variant	Intron 1 of 12	5	NM_194313.4	ENSP00000384433.1
SERPINH1P1	ENST00000419794.1	n.250G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
KIF24	ENST00000684219.1	c.-26+784C>T		intron_variant	Intron 2 of 2			ENSP00000506725.1

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

African (AFR) AF: 0.155 AC: 5080 AN: 32780

American (AMR) AF: 0.473 AC: 19337 AN: 40894

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 14916 AN: 25268

East Asian (EAS) AF: 0.304 AC: 11809 AN: 38800

South Asian (SAS) AF: 0.633 AC: 51808 AN: 81890

European-Finnish (FIN) AF: 0.578 AC: 22267 AN: 38510

Middle Eastern (MID) AF: 0.582 AC: 2385 AN: 4098

European-Non Finnish (NFE) AF: 0.626 AC: 655930 AN: 1048508

Other (OTH) AF: 0.566 AC: 32503 AN: 57446

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

African (AFR) AF: 0.173 AC: 7191 AN: 41546

American (AMR) AF: 0.485 AC: 7423 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1724 AN: 5164

South Asian (SAS) AF: 0.636 AC: 3074 AN: 4830

European-Finnish (FIN) AF: 0.561 AC: 5945 AN: 10600

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

European-Non Finnish (NFE) AF: 0.631 AC: 42898 AN: 67976

Other (OTH) AF: 0.512 AC: 1084 AN: 2116

Alfa AF: 0.536 Hom.: 3117

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
PhyloP100		5.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10972055; hg19: chr9-34318654;