1-245477265-T-G

Variant names:

• chr1-245477265-T-G
• rs10737772
• NM_018012.4:c.1166+57520T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018012.4(KIF26B):​c.1166+57520T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,626 control chromosomes in the GnomAD database, including 32,430 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 0.65 (32430 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1166+57520T>G		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.1166+57520T>G		intron_variant	Intron 4 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 97860 AN: 151506 Hom.: 32412 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.646 AC: 97907 AN: 151626 Hom.: 32430 Cov.: 32 AF XY: 0.649 AC XY: 48068 AN XY: 74086

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.651

Alfa AF: 0.664 Hom.: 34946

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.80

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: rs10737772; hg19: chr1-245640567;