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GeneBe

1-245367244-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_018012.4(KIF26B):c.876C>T(p.Leu292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,608,092 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 6 hom. )

Consequence

KIF26B
NM_018012.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.251
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-245367244-C-T is Benign according to our data. Variant chr1-245367244-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3050204.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.251 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 205 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF26BNM_018012.4 linkuse as main transcriptc.876C>T p.Leu292= synonymous_variant 3/15 ENST00000407071.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF26BENST00000407071.7 linkuse as main transcriptc.876C>T p.Leu292= synonymous_variant 3/151 NM_018012.4 A2Q2KJY2-1
KIF26BENST00000479506.1 linkuse as main transcriptn.650C>T non_coding_transcript_exon_variant 2/41

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00135
AC:
205
AN:
152238
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00425
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000829
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00181
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00103
AC:
244
AN:
236662
Hom.:
2
AF XY:
0.00112
AC XY:
143
AN XY:
128224
show subpopulations
Gnomad AFR exome
AF:
0.000280
Gnomad AMR exome
AF:
0.000874
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000591
Gnomad FIN exome
AF:
0.000192
Gnomad NFE exome
AF:
0.00173
Gnomad OTH exome
AF:
0.000864
GnomAD4 exome
AF:
0.00151
AC:
2201
AN:
1455736
Hom.:
6
Cov.:
32
AF XY:
0.00147
AC XY:
1066
AN XY:
723464
show subpopulations
Gnomad4 AFR exome
AF:
0.000449
Gnomad4 AMR exome
AF:
0.00112
Gnomad4 ASJ exome
AF:
0.0000385
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000436
Gnomad4 FIN exome
AF:
0.000283
Gnomad4 NFE exome
AF:
0.00182
Gnomad4 OTH exome
AF:
0.00111
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00135
AC:
205
AN:
152356
Hom.:
1
Cov.:
32
AF XY:
0.00146
AC XY:
109
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.000192
Gnomad4 AMR
AF:
0.00425
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00181
Gnomad4 OTH
AF:
0.00236
Alfa
AF:
0.00126
Hom.:
1
Bravo
AF:
0.00161

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

KIF26B-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesJul 23, 2019This variant is classified as likely 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
-0.40
Cadd
Benign
6.7
Dann
Benign
0.75

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.

Other links and lift over

dbSNP: rs200520003; hg19: chr1-245530546; API