10-92592178-C-T

Variant names:

• chr10-92592178-C-T
• rs11595187
• ENST00000676647.1:c.-131+349C>T

Variant summary

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

The ENST00000676647.1(KIF11):​c.-131+349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,070 control chromosomes in the GnomAD database, including 755 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 0.091 (755 hom., cov: 32)
• Consequence: KIF11 ENST00000676647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000676647.1	c.-131+349C>T		intron_variant	Intron 1 of 21			ENSP00000503394.1
KIF11	ENST00000676757.1	c.-130-14087C>T		intron_variant	Intron 1 of 21			ENSP00000504289.1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13822 AN: 151952 Hom.: 754 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.0790

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

GnomAD4 genome AF: 0.0910 AC: 13843 AN: 152070 Hom.: 755 Cov.: 32 AF XY: 0.0922 AC XY: 6852 AN XY: 74328

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0498

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0534

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0896 Hom.: 84

Bravo AF: 0.0974

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11595187; hg19: chr10-94351935;