NM_018012.4:c.1166+57520T>G

Variant names:

• chr1-245477265-T-G
• rs10737772
• NM_018012.4:c.1166+57520T>G

Variant summary

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

The NM_018012.4(KIF26B):​c.1166+57520T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,626 control chromosomes in the GnomAD database, including 32,430 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 0.65 (32430 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018012.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	NM_018012.4	MANE Select	c.1166+57520T>G		intron	N/A	NP_060482.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	ENST00000407071.7	TSL:1 MANE Select	c.1166+57520T>G		intron	N/A	ENSP00000385545.2	Q2KJY2-1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97860 AN: 151506 Hom.: 32412 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.646 AC: 97907 AN: 151626 Hom.: 32430 Cov.: 32 AF XY: 0.649 AC XY: 48068 AN XY: 74086

African (AFR) AF: 0.544 AC: 22554 AN: 41438

American (AMR) AF: 0.691 AC: 10550 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3468

East Asian (EAS) AF: 0.714 AC: 3685 AN: 5162

South Asian (SAS) AF: 0.646 AC: 3076 AN: 4760

European-Finnish (FIN) AF: 0.716 AC: 7526 AN: 10516

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 45957 AN: 67704

Other (OTH) AF: 0.651 AC: 1373 AN: 2108

Alfa AF: 0.657 Hom.: 61617

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		0.17
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: rs10737772; hg19: chr1-245640567;