rs4498839

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018012.4(KIF26B):​c.466-9554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,180 control chromosomes in the GnomAD database, including 7,391 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 7391 hom., cov: 32)

Consequence

KIF26B
NM_018012.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF26BNM_018012.4 linkuse as main transcriptc.466-9554T>C intron_variant ENST00000407071.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF26BENST00000407071.7 linkuse as main transcriptc.466-9554T>C intron_variant 1 NM_018012.4 A2Q2KJY2-1
KIF26BENST00000479506.1 linkuse as main transcriptn.239+3364T>C intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.188
AC:
28647
AN:
152062
Hom.:
7346
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.576
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.0179
Gnomad EAS
AF:
0.289
Gnomad SAS
AF:
0.0311
Gnomad FIN
AF:
0.00819
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0114
Gnomad OTH
AF:
0.146
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.189
AC:
28748
AN:
152180
Hom.:
7391
Cov.:
32
AF XY:
0.186
AC XY:
13873
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.576
Gnomad4 AMR
AF:
0.127
Gnomad4 ASJ
AF:
0.0179
Gnomad4 EAS
AF:
0.289
Gnomad4 SAS
AF:
0.0301
Gnomad4 FIN
AF:
0.00819
Gnomad4 NFE
AF:
0.0114
Gnomad4 OTH
AF:
0.149
Alfa
AF:
0.0572
Hom.:
787
Bravo
AF:
0.219
Asia WGS
AF:
0.188
AC:
652
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.6
DANN
Benign
0.66

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: rs4498839; hg19: chr1-245520582; API