rs11579379

Positions:

• chr1-245396843-A-G

Variant summary

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

The NM_018012.4(KIF26B):​c.1000-22736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,026 control chromosomes in the GnomAD database, including 6,441 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 0.23 (6441 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF26B	NM_018012.4	c.1000-22736A>G		intron_variant		ENST00000407071.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26B	ENST00000407071.7	c.1000-22736A>G		intron_variant		1	NM_018012.4	A2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35515 AN: 151906 Hom.: 6416 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.234 AC: 35580 AN: 152026 Hom.: 6441 Cov.: 32 AF XY: 0.233 AC XY: 17317 AN XY: 74298

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.0745

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.211

Alfa AF: 0.129 Hom.: 3344

Bravo AF: 0.249

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.62

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: rs11579379; hg19: chr1-245560145;