rs10924245

Positions:

• chr1-245570306-G-T

Variant summary

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

The NM_018012.4(KIF26B):​c.1350+29356G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,068 control chromosomes in the GnomAD database, including 960 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 0.098 (960 hom., cov: 31)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1350+29356G>T		intron_variant		ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1350+29356G>T		intron_variant		1	NM_018012.4	ENSP00000385545	A2
KIF26B	ENST00000366518.4	c.207+29356G>T		intron_variant		5		ENSP00000355475	P4

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14875 AN: 151950 Hom.: 955 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0980 AC: 14902 AN: 152068 Hom.: 960 Cov.: 31 AF XY: 0.0974 AC XY: 7240 AN XY: 74328

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0864

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0748 Hom.: 699

Bravo AF: 0.103

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.26
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: rs10924245; hg19: chr1-245733608;