rs6656693

Variant names:

• chr1-245172341-G-A
• rs6656693
• NM_018012.4:c.465+15658G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-245172341-G-A
• chr1-245172341-G-C
• chr1-245172341-G-T

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+15658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,922 control chromosomes in the GnomAD database, including 14,356 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 0.40 (14356 hom., cov: 32)
• Consequence: KIF26B NM_018012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF26B	NM_018012.4	c.465+15658G>A		intron_variant	Intron 2 of 14	ENST00000407071.7	NP_060482.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF26B	ENST00000407071.7	c.465+15658G>A		intron_variant	Intron 2 of 14	1	NM_018012.4	ENSP00000385545.2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60409 AN: 151804 Hom.: 14317 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.398 AC: 60496 AN: 151922 Hom.: 14356 Cov.: 32 AF XY: 0.390 AC XY: 28943 AN XY: 74260

African (AFR) AF: 0.669 AC: 27670 AN: 41380

American (AMR) AF: 0.279 AC: 4256 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2332 AN: 5160

South Asian (SAS) AF: 0.282 AC: 1357 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20033 AN: 67958

Other (OTH) AF: 0.359 AC: 756 AN: 2106

Alfa AF: 0.307 Hom.: 14771

Bravo AF: 0.413

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.81
PhyloP100		0.040
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: rs6656693; hg19: chr1-245335643;