chr1-245365113-G-A

Variant names:

• chr1-245365113-G-A
• rs1148917
• NM_018012.4:c.466-1721G>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.466-1721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,126 control chromosomes in the GnomAD database, including 5,696 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 0.24 (5696 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.466-1721G>A		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.466-1721G>A		intron_variant	Intron 2 of 14	1	NM_018012.4	ENSP00000385545.2
KIF26B	ENST00000479506.1	n.240-1721G>A		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36563 AN: 152008 Hom.: 5693 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.240 AC: 36567 AN: 152126 Hom.: 5696 Cov.: 32 AF XY: 0.238 AC XY: 17729 AN XY: 74376

African (AFR) AF: 0.0611 AC: 2535 AN: 41512

American (AMR) AF: 0.341 AC: 5217 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.0532 AC: 275 AN: 5174

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4826

European-Finnish (FIN) AF: 0.273 AC: 2888 AN: 10590

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22506 AN: 67964

Other (OTH) AF: 0.227 AC: 479 AN: 2108

Alfa AF: 0.306 Hom.: 5783

Bravo AF: 0.237

Asia WGS AF: 0.133 AC: 462 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	0.013
DANN	Benign	0.55
PhyloP100		-3.8
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: rs1148917; hg19: chr1-245528415;