10-92592979-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000676647.1(KIF11):c.-131+1150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,332 control chromosomes in the GnomAD database, including 178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.043 (178 hom., cov: 33)
• Consequence: KIF11 ENST00000676647.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -6.23

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 10-92592979-A-G is Benign according to our data. Variant chr10-92592979-A-G is described in ClinVar as [Benign]. Clinvar id is 1221670.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000676647.1	c.-131+1150A>G		intron_variant
KIF11	ENST00000676757.1	c.-130-13286A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6516 AN: 152214 Hom.: 178 Cov.: 33

Gnomad AFR AF: 0.0406

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0813

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0428 AC: 6517 AN: 152332 Hom.: 178 Cov.: 33 AF XY: 0.0444 AC XY: 3308 AN XY: 74496

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0813

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0155 Hom.: 4

Bravo AF: 0.0413

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.064
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74151659; hg19: chr10-94352736;