rs1538472

Variant names:

• chr1-245472757-A-G
• rs1538472
• NM_018012.4:c.1166+53012A>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+53012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,980 control chromosomes in the GnomAD database, including 17,858 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 0.48 (17858 hom., cov: 33)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1166+53012A>G		intron_variant	Intron 4 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1166+53012A>G		intron_variant	Intron 4 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73060 AN: 151862 Hom.: 17848 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.481 AC: 73116 AN: 151980 Hom.: 17858 Cov.: 33 AF XY: 0.478 AC XY: 35522 AN XY: 74284

African (AFR) AF: 0.441 AC: 18295 AN: 41444

American (AMR) AF: 0.470 AC: 7176 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3468

East Asian (EAS) AF: 0.549 AC: 2824 AN: 5146

South Asian (SAS) AF: 0.465 AC: 2234 AN: 4806

European-Finnish (FIN) AF: 0.496 AC: 5227 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34476 AN: 67988

Other (OTH) AF: 0.482 AC: 1018 AN: 2114

Alfa AF: 0.494 Hom.: 31559

Bravo AF: 0.477

Asia WGS AF: 0.477 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.048
DANN	Benign	0.50
PhyloP100		-1.0
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: rs1538472; hg19: chr1-245636059;