rs12567206

Positions:

• chr1-245158870-G-T

Variant summary

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

The NM_018012.4(KIF26B):​c.465+2187G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 (161 hom., cov: 0)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF26B	NM_018012.4	c.465+2187G>T		intron_variant		ENST00000407071.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26B	ENST00000407071.7	c.465+2187G>T		intron_variant		1	NM_018012.4	A2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 6221 AN: 42460 Hom.: 159 Cov.: 0

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00741

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.147 AC: 6252 AN: 42556 Hom.: 161 Cov.: 0 AF XY: 0.153 AC XY: 3157 AN XY: 20666

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.161

Alfa AF: 0.611 Hom.: 6072

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.54

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: rs12567206; hg19: chr1-245322172;