1-245409250-A-G

Position:

• chr1-245409250-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1000-10329A>G		intron_variant		ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1000-10329A>G		intron_variant		1	NM_018012.4	ENSP00000385545	A2

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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.692

Alfa AF: 0.659 Hom.: 66757

Bravo AF: 0.721

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.39

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: rs676292; hg19: chr1-245572552;