chr1-245409250-A-G

Variant names:

• chr1-245409250-A-G
• rs676292
• NM_018012.4:c.1000-10329A>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.1000-10329A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,186 control chromosomes in the GnomAD database, including 39,567 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 0.71 (39567 hom., cov: 34)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018012.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	NM_018012.4	MANE Select	c.1000-10329A>G		intron	N/A	NP_060482.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	ENST00000407071.7	TSL:1 MANE Select	c.1000-10329A>G		intron	N/A	ENSP00000385545.2	Q2KJY2-1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108643 AN: 152068 Hom.: 39530 Cov.: 34

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.714 AC: 108729 AN: 152186 Hom.: 39567 Cov.: 34 AF XY: 0.718 AC XY: 53413 AN XY: 74378

African (AFR) AF: 0.863 AC: 35841 AN: 41544

American (AMR) AF: 0.699 AC: 10683 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.612 AC: 3165 AN: 5168

South Asian (SAS) AF: 0.729 AC: 3512 AN: 4820

European-Finnish (FIN) AF: 0.693 AC: 7334 AN: 10576

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43891 AN: 68006

Other (OTH) AF: 0.692 AC: 1459 AN: 2108

Alfa AF: 0.663 Hom.: 97062

Bravo AF: 0.721

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.39
PhyloP100		0.57
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: rs676292; hg19: chr1-245572552;