rs4658749

Variant names:

• chr1-245319044-A-C
• rs4658749
• NM_018012.4:c.466-47790A>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.466-47790A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,038 control chromosomes in the GnomAD database, including 12,166 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 0.33 (12166 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.466-47790A>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.466-47790A>C		intron_variant	Intron 2 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50730 AN: 151924 Hom.: 12130 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.283

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.334 AC: 50836 AN: 152038 Hom.: 12166 Cov.: 32 AF XY: 0.331 AC XY: 24646 AN XY: 74348

African (AFR) AF: 0.664 AC: 27544 AN: 41466

American (AMR) AF: 0.399 AC: 6092 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1670 AN: 5174

South Asian (SAS) AF: 0.182 AC: 876 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1515 AN: 10606

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11935 AN: 67920

Other (OTH) AF: 0.283 AC: 596 AN: 2108

Alfa AF: 0.216 Hom.: 6497

Bravo AF: 0.371

Asia WGS AF: 0.265 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.15
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: rs4658749; hg19: chr1-245482346;