Variant chr10-92593066-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000676647.1(KIF11):c.-131+1237C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,336 control chromosomes in the GnomAD database, including 1,027 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1027 hom., cov: 33)

Consequence

KIF11
ENST00000676647.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0740

Variant links:

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]

KIF11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 10-92593066-C-G is Benign according to our data. Variant chr10-92593066-C-G is described in ClinVar as [Benign]. Clinvar id is 1289364.Status of the report is criteria_provided_single_submitter, 1 stars.

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF11	ENST00000676647.1 linkuse as main transcript	c.-131+1237C>G		intron_variant
KIF11	ENST00000676757.1 linkuse as main transcript	c.-130-13199C>G		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16173

AN:

152218

Hom.:

1022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.0498

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.0533

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0796

Gnomad OTH

AF:

0.0917

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

GnomAD4 genome

AF:

0.106

AC:

16214

AN:

152336

Hom.:

1027

Cov.:

AF XY:

0.108

AC XY:

8014

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.154

Gnomad4 ASJ

AF:

0.0498

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.165

Gnomad4 FIN

AF:

0.0533

Gnomad4 NFE

AF:

0.0797

Gnomad4 OTH

AF:

0.0936

Alfa

AF:

0.0970

Hom.:

106

Bravo

AF:

0.115

Asia WGS

AF:

0.136

AC:

473

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-0.77

CADD

Benign

5.6

DANN

Benign

0.66

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over