rs10924245

Variant names:

• chr1-245570306-G-T
• rs10924245
• NM_018012.4:c.1350+29356G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.85).
• 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 rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1350+29356G>T		intron_variant	Intron 5 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1350+29356G>T		intron_variant	Intron 5 of 14	1	NM_018012.4	ENSP00000385545.2
KIF26B	ENST00000366518.4	c.207+29356G>T		intron_variant	Intron 2 of 11	5		ENSP00000355475.4

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

African (AFR) AF: 0.172 AC: 7132 AN: 41446

American (AMR) AF: 0.0864 AC: 1319 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0629 AC: 218 AN: 3468

East Asian (EAS) AF: 0.0770 AC: 398 AN: 5172

South Asian (SAS) AF: 0.0984 AC: 474 AN: 4816

European-Finnish (FIN) AF: 0.0516 AC: 546 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0660 AC: 4485 AN: 67994

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.0798 Hom.: 1880

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
PhyloP100		-0.058
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: rs10924245; hg19: chr1-245733608;