rs11187094

chr10-92608421-G-Achr10-92608421-G-T

Variant summary

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

The NM_004523.4(KIF11):c.388-599G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,702 control chromosomes in the GnomAD database, including 4,019 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 0.20 (4019 hom., cov: 31)
• Consequence: KIF11 NM_004523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.951

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF11	NM_004523.4	c.388-599G>A		intron_variant		ENST00000260731.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000260731.5	c.388-599G>A		intron_variant		1	NM_004523.4	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30114 AN: 151590 Hom.: 4023 Cov.: 31

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.198 AC: 30107 AN: 151702 Hom.: 4019 Cov.: 31 AF XY: 0.206 AC XY: 15297 AN XY: 74114

Gnomad4 AFR AF: 0.0609

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.201

Alfa AF: 0.211 Hom.: 5524

Bravo AF: 0.185

Asia WGS AF: 0.450 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.63
Dann	Benign	0.68

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: rs11187094; hg19: chr10-94368178;