Variant rs3820246 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_018012.4(KIF26B):c.3444G>A(p.Pro1148Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 1,613,346 control chromosomes in the GnomAD database, including 1,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.026 ( 176 hom., cov: 33)

Exomes 𝑓: 0.021 ( 1410 hom. )

Consequence

KIF26B
NM_018012.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.65

Variant links:

Genes affected

KIF26B (HGNC:25484): (kinesin family member 26B) The protein encoded by this gene is an intracellular motor protein thought to transport organelles along microtubules. The encoded protein is required for kidney development. Elevated levels of this protein have been found in some breast and colorectal cancers. [provided by RefSeq, Mar 2017]

KIF26B links:

LOC105373265 (HGNC:):

LOC105373265 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-245686427-G-A is Benign according to our data. Variant chr1-245686427-G-A is described in ClinVar as [Benign]. Clinvar id is 403008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-245686427-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.65 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF26B	NM_018012.4 link	c.3444G>A	p.Pro1148Pro	synonymous_variant	12/15	ENST00000407071.7	NP_060482.2	Q2KJY2-1
LOC105373265	XR_007066988.1 link	n.657-1976C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KIF26B	ENST00000407071.7 link	c.3444G>A	p.Pro1148Pro	synonymous_variant	12/15	1	NM_018012.4	ENSP00000385545.2	Q2KJY2-1
KIF26B	ENST00000366518.4 link	c.2301G>A	p.Pro767Pro	synonymous_variant	9/12	5		ENSP00000355475.4	B7WPD9
KIF26B	ENST00000483253.1 link	n.1375G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.0257

AC:

3903

AN:

152116

Hom.:

169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.00836

Gnomad EAS

AF:

0.108

Gnomad SAS

AF:

0.0350

Gnomad FIN

AF:

0.00386

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0119

Gnomad OTH

AF:

0.0278

GnomAD3 exomes

AF:

0.0488

AC:

12143

AN:

248938

Hom.:

1055

AF XY:

0.0416

AC XY:

5626

AN XY:

135198

show subpopulations

Gnomad AFR exome

AF:

0.0149

Gnomad AMR exome

AF:

0.211

Gnomad ASJ exome

AF:

0.00577

Gnomad EAS exome

AF:

0.116

Gnomad SAS exome

AF:

0.0304

Gnomad FIN exome

AF:

0.00557

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.0365

GnomAD4 exome

AF:

0.0210

AC:

30712

AN:

1461110

Hom.:

1410

Cov.:

AF XY:

0.0203

AC XY:

14777

AN XY:

726860

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.00578

Gnomad4 EAS exome

AF:

0.0943

Gnomad4 SAS exome

AF:

0.0292

Gnomad4 FIN exome

AF:

0.00617

Gnomad4 NFE exome

AF:

0.0118

Gnomad4 OTH exome

AF:

0.0231

GnomAD4 genome

AF:

0.0258

AC:

3932

AN:

152236

Hom.:

176

Cov.:

AF XY:

0.0277

AC XY:

2063

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0160

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.00836

Gnomad4 EAS

AF:

0.108

Gnomad4 SAS

AF:

0.0346

Gnomad4 FIN

AF:

0.00386

Gnomad4 NFE

AF:

0.0119

Gnomad4 OTH

AF:

0.0275

Alfa

AF:

0.0186

Hom.:

181

Bravo

AF:

0.0350

Asia WGS

AF:

0.0740

AC:

257

AN:

3478

EpiCase

AF:

0.0110

EpiControl

AF:

0.00966

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

KIF26B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 05, 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). -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.065

DANN

Benign

0.52

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