rs10736069

chr10-92635636-T-Cchr10-92635636-T-G

Variant summary

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

The NM_004523.4(KIF11):c.1876-1548T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,082 control chromosomes in the GnomAD database, including 38,545 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 0.70 (38545 hom., cov: 32)
• Consequence: KIF11 NM_004523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

Genes affected

KIF11 (HGNC:6388): (kinesin family member 11) This gene encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF11	NM_004523.4	c.1876-1548T>C		intron_variant		ENST00000260731.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000260731.5	c.1876-1548T>C		intron_variant		1	NM_004523.4	P1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106244 AN: 151964 Hom.: 38490 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.668

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.699 AC: 106358 AN: 152082 Hom.: 38545 Cov.: 32 AF XY: 0.697 AC XY: 51850 AN XY: 74340

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.667

Alfa AF: 0.640 Hom.: 3766

Bravo AF: 0.714

Asia WGS AF: 0.806 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.5
Dann	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs10736069; hg19: chr10-94395393;