Variant rs17107764 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004523.4(KIF11):c.1702+9A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 1,562,260 control chromosomes in the GnomAD database, including 8,146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 3604 hom., cov: 32)

Exomes 𝑓: 0.054 ( 4542 hom. )

Consequence

KIF11
NM_004523.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.745

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 10-92632702-A-T is Benign according to our data. Variant chr10-92632702-A-T is described in ClinVar as [Benign]. Clinvar id is 259408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-92632702-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4 linkuse as main transcript	c.1702+9A>T		intron_variant		ENST00000260731.5	NP_004514.2	P52732

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5 linkuse as main transcript	c.1702+9A>T		intron_variant		1	NM_004523.4	ENSP00000260731.3		P52732

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22672

AN:

151916

Hom.:

3598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.0949

Gnomad SAS

AF:

0.0786

Gnomad FIN

AF:

0.00775

Gnomad MID

AF:

0.115

Gnomad NFE

AF:

0.0409

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.0804

AC:

18194

AN:

226312

Hom.:

1766

AF XY:

0.0736

AC XY:

9010

AN XY:

122448

show subpopulations

Gnomad AFR exome

AF:

0.410

Gnomad AMR exome

AF:

0.0972

Gnomad ASJ exome

AF:

0.0484

Gnomad EAS exome

AF:

0.115

Gnomad SAS exome

AF:

0.0712

Gnomad FIN exome

AF:

0.00886

Gnomad NFE exome

AF:

0.0411

Gnomad OTH exome

AF:

0.0631

GnomAD4 exome

AF:

0.0540

AC:

76140

AN:

1410226

Hom.:

4542

Cov.:

AF XY:

0.0533

AC XY:

37401

AN XY:

701202

show subpopulations

Gnomad4 AFR exome

AF:

0.413

Gnomad4 AMR exome

AF:

0.0946

Gnomad4 ASJ exome

AF:

0.0491

Gnomad4 EAS exome

AF:

0.0895

Gnomad4 SAS exome

AF:

0.0697

Gnomad4 FIN exome

AF:

0.0111

Gnomad4 NFE exome

AF:

0.0407

Gnomad4 OTH exome

AF:

0.0687

GnomAD4 genome

AF:

0.149

AC:

22713

AN:

152034

Hom.:

3604

Cov.:

AF XY:

0.144

AC XY:

10736

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.398

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0493

Gnomad4 EAS

AF:

0.0950

Gnomad4 SAS

AF:

0.0774

Gnomad4 FIN

AF:

0.00775

Gnomad4 NFE

AF:

0.0409

Gnomad4 OTH

AF:

0.134

Alfa

AF:

0.0793

Hom.:

279

Bravo

AF:

0.166

Asia WGS

AF:

0.108

AC:

377

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.0

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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