chr1-245484059-G-A

Position:

• chr1-245484059-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KIF26B	NM_018012.4	c.1167-56708G>A		intron_variant		ENST00000407071.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26B	ENST00000407071.7	c.1167-56708G>A		intron_variant		1	NM_018012.4	A2

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

Gnomad4 AFR AF: 0.0184

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0653 Hom.: 256

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs12121903; hg19: chr1-245647361;