10-92634645-T-G

Position:

• chr10-92634645-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004523.4(KIF11):​c.1875+850T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,076 control chromosomes in the GnomAD database, including 8,252 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 0.31 (8252 hom., cov: 32)
• Consequence: KIF11 NM_004523.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF11	NM_004523.4	c.1875+850T>G		intron_variant		ENST00000260731.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000260731.5	c.1875+850T>G		intron_variant		1	NM_004523.4	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47172 AN: 151958 Hom.: 8250 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.310 AC: 47191 AN: 152076 Hom.: 8252 Cov.: 32 AF XY: 0.315 AC XY: 23401 AN XY: 74322

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.321

Alfa AF: 0.317 Hom.: 997

Bravo AF: 0.298

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	18
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.46		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.46		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs10882095; hg19: chr10-94394402;