Variant 6-168030818-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_030615.4(KIF25):c.138G>A(p.Val46Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00774 in 1,613,160 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 74 hom. )

Consequence

KIF25
NM_030615.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.806

Variant links:

Genes affected

KIF25 (HGNC:6390): (kinesin family member 25) The protein encoded by this gene is a member of the kinesin-like protein family. Protein family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. However, the particular function of this gene product has not yet been determined. Two alternatively spliced transcript variants which encode products have been described. Other splice variants have been found that lack exon 2 and the initiation codon for translation. [provided by RefSeq, Jul 2008]

KIF25 links:

KIF25 (HGNC:):

KIF25 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 6-168030818-G-A is Benign according to our data. Variant chr6-168030818-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657136.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.806 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF25	NM_030615.4 linkuse as main transcript	c.138G>A	p.Val46Val	synonymous_variant	7/13	ENST00000643607.3	NP_085118.2	Q9UIL4-1
KIF25	NM_005355.5 linkuse as main transcript	c.138G>A	p.Val46Val	synonymous_variant	7/12		NP_005346.3	Q9UIL4-2
KIF25	XM_047418749.1 linkuse as main transcript	c.138G>A	p.Val46Val	synonymous_variant	5/11		XP_047274705.1
KIF25	XM_011535803.4 linkuse as main transcript	c.138G>A	p.Val46Val	synonymous_variant	5/10		XP_011534105.1	Q9UIL4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF25	ENST00000643607.3 linkuse as main transcript	c.138G>A	p.Val46Val	synonymous_variant	7/13		NM_030615.4	ENSP00000496229.1		Q9UIL4-1

Frequencies

GnomAD3 genomes

AF:

0.00544

AC:

828

AN:

152076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00186

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00413

Gnomad ASJ

AF:

0.0317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.00293

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00759

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00597

AC:

1497

AN:

250738

Hom.:

AF XY:

0.00615

AC XY:

834

AN XY:

135536

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00311

Gnomad ASJ exome

AF:

0.0296

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00295

Gnomad FIN exome

AF:

0.00324

Gnomad NFE exome

AF:

0.00756

Gnomad OTH exome

AF:

0.00787

GnomAD4 exome

AF:

0.00798

AC:

11653

AN:

1460966

Hom.:

Cov.:

AF XY:

0.00782

AC XY:

5687

AN XY:

726840

show subpopulations

Gnomad4 AFR exome

AF:

0.00138

Gnomad4 AMR exome

AF:

0.00300

Gnomad4 ASJ exome

AF:

0.0312

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00414

Gnomad4 FIN exome

AF:

0.00464

Gnomad4 NFE exome

AF:

0.00858

Gnomad4 OTH exome

AF:

0.00810

GnomAD4 genome

AF:

0.00543

AC:

826

AN:

152194

Hom.:

Cov.:

AF XY:

0.00501

AC XY:

373

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00185

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.0317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00293

Gnomad4 NFE

AF:

0.00760

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00801

Hom.:

Bravo

AF:

0.00539

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00776

EpiControl

AF:

0.00742

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

KIF25: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.32

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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