rs12129648

Variant names:

• chr1-245208190-A-G
• rs12129648
• NM_018012.4:c.465+51507A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018012.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	NM_018012.4	MANE Select	c.465+51507A>G		intron	N/A	NP_060482.2
	KIF26B-AS1	NR_151721.1		n.477-1397T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26B	ENST00000407071.7	TSL:1 MANE Select	c.465+51507A>G		intron	N/A	ENSP00000385545.2
	KIF26B-AS1	ENST00000446321.1	TSL:2	n.461-1397T>C		intron	N/A

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

African (AFR) AF: 0.128 AC: 5300 AN: 41522

American (AMR) AF: 0.630 AC: 9643 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2202 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1912 AN: 5176

South Asian (SAS) AF: 0.586 AC: 2820 AN: 4814

European-Finnish (FIN) AF: 0.698 AC: 7365 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.698 AC: 47454 AN: 67964

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.634 Hom.: 101635

Bravo AF: 0.497

Asia WGS AF: 0.462 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		-0.037
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: rs12129648; hg19: chr1-245371492;