Variant 5-155015017-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001099293.3(KIF4B):c.1158A>G(p.Gln386Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,614,178 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.016 ( 65 hom., cov: 32)

Exomes 𝑓: 0.013 ( 514 hom. )

Consequence

KIF4B
NM_001099293.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.172

Variant links:

Genes affected

KIF4B (HGNC:6322): (kinesin family member 4B) This gene is an intronless retrocopy of kinesin family member 4A. The protein encoded by this gene is a microtubule-based motor protein that plays vital roles in anaphase spindle dynamics and cytokinesis. [provided by RefSeq, Jul 2016]

KIF4B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-155015017-A-G is Benign according to our data. Variant chr5-155015017-A-G is described in ClinVar as [Benign]. Clinvar id is 3059859.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.172 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF4B	NM_001099293.3 linkuse as main transcript	c.1158A>G	p.Gln386Gln	synonymous_variant	1/1	ENST00000435029.6	NP_001092763.1	Q2VIQ3B4DYE2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF4B	ENST00000435029.6 linkuse as main transcript	c.1158A>G	p.Gln386Gln	synonymous_variant	1/1	6	NM_001099293.3	ENSP00000387875.3		Q2VIQ3

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

2448

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00374

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00540

Gnomad SAS

AF:

0.00683

Gnomad FIN

AF:

0.0314

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00997

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0276

AC:

6938

AN:

251476

Hom.:

372

AF XY:

0.0229

AC XY:

3119

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.00320

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.00407

Gnomad EAS exome

AF:

0.00603

Gnomad SAS exome

AF:

0.00493

Gnomad FIN exome

AF:

0.0321

Gnomad NFE exome

AF:

0.00952

Gnomad OTH exome

AF:

0.0213

GnomAD4 exome

AF:

0.0130

AC:

19031

AN:

1461868

Hom.:

514

Cov.:

AF XY:

0.0123

AC XY:

8941

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.00320

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.00375

Gnomad4 EAS exome

AF:

0.00433

Gnomad4 SAS exome

AF:

0.00543

Gnomad4 FIN exome

AF:

0.0275

Gnomad4 NFE exome

AF:

0.00929

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.0161

AC:

2447

AN:

152310

Hom.:

Cov.:

AF XY:

0.0176

AC XY:

1313

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00373

Gnomad4 AMR

AF:

0.0726

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00522

Gnomad4 SAS

AF:

0.00663

Gnomad4 FIN

AF:

0.0314

Gnomad4 NFE

AF:

0.00997

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.0100

Hom.:

Bravo

AF:

0.0215

Asia WGS

AF:

0.00866

AC:

AN:

3478

EpiCase

AF:

0.00927

EpiControl

AF:

0.00901

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

KIF4B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 29, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

DANN

Benign

0.30

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