rs1173837

Variant names:

• chr1-245393992-A-C
• rs1173837
• NM_018012.4:c.1000-25587A>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.1000-25587A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,066 control chromosomes in the GnomAD database, including 32,487 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 (32487 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1000-25587A>C		intron_variant	Intron 3 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1000-25587A>C		intron_variant	Intron 3 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99327 AN: 151948 Hom.: 32467 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.654 AC: 99397 AN: 152066 Hom.: 32487 Cov.: 32 AF XY: 0.657 AC XY: 48829 AN XY: 74324

African (AFR) AF: 0.671 AC: 27827 AN: 41476

American (AMR) AF: 0.680 AC: 10390 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3231 AN: 5170

South Asian (SAS) AF: 0.708 AC: 3413 AN: 4818

European-Finnish (FIN) AF: 0.681 AC: 7196 AN: 10570

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43267 AN: 67964

Other (OTH) AF: 0.643 AC: 1356 AN: 2108

Alfa AF: 0.644 Hom.: 125405

Bravo AF: 0.655

Asia WGS AF: 0.656 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.84
PhyloP100		-0.53
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: rs1173837; hg19: chr1-245557294;