rs12121903

Variant names:

• chr1-245484059-G-A
• rs12121903
• NM_018012.4:c.1167-56708G>A

Variant summary

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

The NM_018012.4(KIF26B):​c.1167-56708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 151,478 control chromosomes in the GnomAD database, including 446 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 0.058 (446 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1167-56708G>A		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.1167-56708G>A		intron_variant	Intron 4 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8864 AN: 151360 Hom.: 447 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0654

Gnomad OTH AF: 0.0582

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

GnomAD4 genome AF: 0.0585 AC: 8854 AN: 151478 Hom.: 446 Cov.: 32 AF XY: 0.0609 AC XY: 4505 AN XY: 74016

African (AFR) AF: 0.0184 AC: 761 AN: 41388

American (AMR) AF: 0.0832 AC: 1267 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3468

East Asian (EAS) AF: 0.132 AC: 681 AN: 5164

South Asian (SAS) AF: 0.0952 AC: 449 AN: 4718

European-Finnish (FIN) AF: 0.0746 AC: 782 AN: 10478

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4426 AN: 67734

Other (OTH) AF: 0.0581 AC: 122 AN: 2100

Alfa AF: 0.0654 Hom.: 282

Bravo AF: 0.0575

Asia WGS AF: 0.118 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.13
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: rs12121903; hg19: chr1-245647361;