Variant rs12259474 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.309-18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 1,499,214 control chromosomes in the GnomAD database, including 6,720 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 3362 hom., cov: 32)

Exomes 𝑓: 0.032 ( 3358 hom. )

Consequence

KIF11
NM_004523.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.09

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=-0.85).

BP6

Variant 10-92607141-A-G is Benign according to our data. Variant chr10-92607141-A-G is described in ClinVar as [Benign]. Clinvar id is 259411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-92607141-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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.309-18A>G		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.309-18A>G		intron_variant		1	NM_004523.4	ENSP00000260731.3		P52732

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19514

AN:

152042

Hom.:

3356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.392

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0696

Gnomad ASJ

AF:

0.0352

Gnomad EAS

AF:

0.0526

Gnomad SAS

AF:

0.0652

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0178

Gnomad OTH

AF:

0.114

GnomAD3 exomes

AF:

0.0522

AC:

12910

AN:

247138

Hom.:

1465

AF XY:

0.0466

AC XY:

6239

AN XY:

133760

show subpopulations

Gnomad AFR exome

AF:

0.401

Gnomad AMR exome

AF:

0.0316

Gnomad ASJ exome

AF:

0.0319

Gnomad EAS exome

AF:

0.0601

Gnomad SAS exome

AF:

0.0550

Gnomad FIN exome

AF:

0.00195

Gnomad NFE exome

AF:

0.0190

Gnomad OTH exome

AF:

0.0387

GnomAD4 exome

AF:

0.0316

AC:

42626

AN:

1347054

Hom.:

3358

Cov.:

AF XY:

0.0314

AC XY:

21259

AN XY:

676514

show subpopulations

Gnomad4 AFR exome

AF:

0.412

Gnomad4 AMR exome

AF:

0.0342

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.0475

Gnomad4 SAS exome

AF:

0.0574

Gnomad4 FIN exome

AF:

0.00278

Gnomad4 NFE exome

AF:

0.0172

Gnomad4 OTH exome

AF:

0.0511

GnomAD4 genome

AF:

0.128

AC:

19548

AN:

152160

Hom.:

3362

Cov.:

AF XY:

0.124

AC XY:

9222

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.392

Gnomad4 AMR

AF:

0.0694

Gnomad4 ASJ

AF:

0.0352

Gnomad4 EAS

AF:

0.0527

Gnomad4 SAS

AF:

0.0640

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.0178

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.0642

Hom.:

255

Bravo

AF:

0.144

Asia WGS

AF:

0.0790

AC:

276

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 08, 2018	- -

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

-0.85

CADD

Benign

3.5

DANN

Benign

0.67

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