rs10754459

Variant names:

• chr1-245622206-T-C
• rs10754459
• NM_018012.4:c.2098+10230T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018012.4(KIF26B):​c.2098+10230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,220 control chromosomes in the GnomAD database, including 4,033 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 0.22 (4033 hom., cov: 33)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.2098+10230T>C		intron_variant	Intron 9 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.2098+10230T>C		intron_variant	Intron 9 of 14	1	NM_018012.4	ENSP00000385545.2
KIF26B	ENST00000366518.4	c.955+10230T>C		intron_variant	Intron 6 of 11	5		ENSP00000355475.4

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34136 AN: 152102 Hom.: 4026 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.224 AC: 34161 AN: 152220 Hom.: 4033 Cov.: 33 AF XY: 0.226 AC XY: 16839 AN XY: 74424

African (AFR) AF: 0.184 AC: 7652 AN: 41556

American (AMR) AF: 0.171 AC: 2612 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3464

East Asian (EAS) AF: 0.377 AC: 1953 AN: 5176

South Asian (SAS) AF: 0.305 AC: 1469 AN: 4824

European-Finnish (FIN) AF: 0.283 AC: 2994 AN: 10592

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15983 AN: 67996

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.232 Hom.: 16009

Bravo AF: 0.215

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		0.043
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: rs10754459; hg19: chr1-245785508;