rs12129648

chr1-245208190-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.465+51507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,108 control chromosomes in the GnomAD database, including 25,212 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 0.52 (25212 hom., cov: 33)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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]

KIF26B-AS1 (HGNC:41098): (KIF26B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF26B	NM_018012.4	c.465+51507A>G		intron_variant		ENST00000407071.7
KIF26B-AS1	NR_151721.1	n.477-1397T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26B	ENST00000407071.7	c.465+51507A>G		intron_variant		1	NM_018012.4	A2
KIF26B-AS1	ENST00000446321.1	n.461-1397T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78742 AN: 151988 Hom.: 25201 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.518 AC: 78760 AN: 152108 Hom.: 25212 Cov.: 33 AF XY: 0.519 AC XY: 38576 AN XY: 74354

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.555

Alfa AF: 0.667 Hom.: 67980

Bravo AF: 0.497

Asia WGS AF: 0.462 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	13
Dann	Benign	0.65

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: rs12129648; hg19: chr1-245371492;