rs4498839

Variant names:

• chr1-245357280-T-C
• rs4498839
• NM_018012.4:c.466-9554T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.466-9554T>C		intron_variant	Intron 2 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.466-9554T>C		intron_variant	Intron 2 of 14	1	NM_018012.4	ENSP00000385545.2
KIF26B	ENST00000479506.1	n.239+3364T>C		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28647 AN: 152062 Hom.: 7346 Cov.: 32

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

African (AFR) AF: 0.576 AC: 23901 AN: 41460

American (AMR) AF: 0.127 AC: 1936 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1496 AN: 5172

South Asian (SAS) AF: 0.0301 AC: 145 AN: 4822

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10622

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 773 AN: 68020

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.0545 Hom.: 826

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
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4498839; hg19: chr1-245520582;