Variant rs138267534 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_004523.4(KIF11):c.*19A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00427 in 1,591,102 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0044 ( 24 hom. )

Consequence

KIF11
NM_004523.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.60

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 10-92653815-A-G is Benign according to our data. Variant chr10-92653815-A-G is described in ClinVar as [Benign]. Clinvar id is 259407.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-92653815-A-G is described in Lovd as [Benign].

BS2

High AC in GnomAd4 at 393 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF11	NM_004523.4 linkuse as main transcript	c.*19A>G		3_prime_UTR_variant	22/22	ENST00000260731.5	NP_004514.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF11	ENST00000260731.5 linkuse as main transcript	c.*19A>G		3_prime_UTR_variant	22/22	1	NM_004523.4	ENSP00000260731	P1

Frequencies

GnomAD3 genomes

AF:

0.00258

AC:

393

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00223

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00417

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00290

AC:

664

AN:

229208

Hom.:

AF XY:

0.00297

AC XY:

370

AN XY:

124628

show subpopulations

Gnomad AFR exome

AF:

0.000830

Gnomad AMR exome

AF:

0.00368

Gnomad ASJ exome

AF:

0.00214

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000711

Gnomad FIN exome

AF:

0.00119

Gnomad NFE exome

AF:

0.00442

Gnomad OTH exome

AF:

0.00222

GnomAD4 exome

AF:

0.00444

AC:

6395

AN:

1438778

Hom.:

Cov.:

AF XY:

0.00430

AC XY:

3076

AN XY:

716012

show subpopulations

Gnomad4 AFR exome

AF:

0.000695

Gnomad4 AMR exome

AF:

0.00328

Gnomad4 ASJ exome

AF:

0.00170

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000751

Gnomad4 FIN exome

AF:

0.00127

Gnomad4 NFE exome

AF:

0.00532

Gnomad4 OTH exome

AF:

0.00327

GnomAD4 genome

AF:

0.00258

AC:

393

AN:

152324

Hom.:

Cov.:

AF XY:

0.00226

AC XY:

168

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00222

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00417

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00269

Hom.:

Bravo

AF:

0.00296

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

-0.69

CADD

Benign

9.5

DANN

Benign

0.81

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