Variant 1-245687987-G-T 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.5004G>T(p.Ser1668=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 1,574,508 control chromosomes in the GnomAD database, including 1,408 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 180 hom., cov: 33)

Exomes 𝑓: 0.021 ( 1228 hom. )

Consequence

KIF26B
NM_018012.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.07

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=-0.88).

BP6

Variant 1-245687987-G-T is Benign according to our data. Variant chr1-245687987-G-T is described in ClinVar as [Benign]. Clinvar id is 403010.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF26B	NM_018012.4 linkuse as main transcript	c.5004G>T	p.Ser1668=	synonymous_variant	12/15	ENST00000407071.7
LOC105373265	XR_007066988.1 linkuse as main transcript	n.657-3536C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26B	ENST00000407071.7 linkuse as main transcript	c.5004G>T	p.Ser1668=	synonymous_variant	12/15	1	NM_018012.4	A2	Q2KJY2-1
KIF26B	ENST00000366518.4 linkuse as main transcript	c.3861G>T	p.Ser1287=	synonymous_variant	9/12	5		P4

Frequencies

GnomAD3 genomes

AF:

0.0236

AC:

3591

AN:

152194

Hom.:

177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00579

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.00662

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.0515

Gnomad FIN

AF:

0.00386

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0122

Gnomad OTH

AF:

0.0254

GnomAD3 exomes

AF:

0.0541

AC:

9511

AN:

175710

Hom.:

810

AF XY:

0.0470

AC XY:

4506

AN XY:

95820

show subpopulations

Gnomad AFR exome

AF:

0.00443

Gnomad AMR exome

AF:

0.205

Gnomad ASJ exome

AF:

0.00450

Gnomad EAS exome

AF:

0.126

Gnomad SAS exome

AF:

0.0456

Gnomad FIN exome

AF:

0.00525

Gnomad NFE exome

AF:

0.0117

Gnomad OTH exome

AF:

0.0378

GnomAD4 exome

AF:

0.0210

AC:

29833

AN:

1422196

Hom.:

1228

Cov.:

AF XY:

0.0209

AC XY:

14697

AN XY:

703834

show subpopulations

Gnomad4 AFR exome

AF:

0.00388

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.00467

Gnomad4 EAS exome

AF:

0.0972

Gnomad4 SAS exome

AF:

0.0429

Gnomad4 FIN exome

AF:

0.00597

Gnomad4 NFE exome

AF:

0.0123

Gnomad4 OTH exome

AF:

0.0232

GnomAD4 genome

AF:

0.0236

AC:

3601

AN:

152312

Hom.:

180

Cov.:

AF XY:

0.0257

AC XY:

1913

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00577

Gnomad4 AMR

AF:

0.103

Gnomad4 ASJ

AF:

0.00662

Gnomad4 EAS

AF:

0.113

Gnomad4 SAS

AF:

0.0512

Gnomad4 FIN

AF:

0.00386

Gnomad4 NFE

AF:

0.0122

Gnomad4 OTH

AF:

0.0256

Alfa

AF:

0.0100

Hom.:

Bravo

AF:

0.0326

Asia WGS

AF:

0.0810

AC:

283

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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, criteria provided, single submitter

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.032

DANN

Benign

0.63

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