1-245414046-T-C

Variant names:

• chr1-245414046-T-C
• rs1093960
• NM_018012.4:c.1000-5533T>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.1000-5533T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,158 control chromosomes in the GnomAD database, including 31,687 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 0.64 (31687 hom., cov: 34)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.1000-5533T>C		intron_variant	Intron 3 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.1000-5533T>C		intron_variant	Intron 3 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97217 AN: 152040 Hom.: 31668 Cov.: 34

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.639 AC: 97277 AN: 152158 Hom.: 31687 Cov.: 34 AF XY: 0.635 AC XY: 47258 AN XY: 74380

African (AFR) AF: 0.635 AC: 26379 AN: 41526

American (AMR) AF: 0.535 AC: 8185 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1621 AN: 5146

South Asian (SAS) AF: 0.657 AC: 3164 AN: 4816

European-Finnish (FIN) AF: 0.656 AC: 6943 AN: 10586

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46513 AN: 67996

Other (OTH) AF: 0.658 AC: 1393 AN: 2116

Alfa AF: 0.637 Hom.: 8960

Bravo AF: 0.625

Asia WGS AF: 0.523 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.61
PhyloP100		0.087
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: rs1093960; hg19: chr1-245577348;