NM_001265577.2:c.1238+155C>T

Variant names:

• chr17-44932518-G-A
• rs744281
• NM_001265577.2:c.1238+155C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001265577.2(KIF18B):​c.1238+155C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 622,682 control chromosomes in the GnomAD database, including 53,186 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 0.42 (13735 hom., cov: 32)
  • Exomes 𝑓: 0.41 (39451 hom.)
• Consequence: KIF18B NM_001265577.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 6 publications found

Genes affected

KIF18B (HGNC:27102): (kinesin family member 18B) Enables cytoskeletal motor activity and kinesin binding activity. Involved in microtubule depolymerization; mitotic cell cycle; and regulation of cell division. Located in cytosol; microtubule; and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001265577.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF18B	NM_001265577.2	MANE Select	c.1238+155C>T		intron	N/A	NP_001252506.1
	KIF18B	NM_001264573.2		c.1238+155C>T		intron	N/A	NP_001251503.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF18B	ENST00000593135.6	TSL:5 MANE Select	c.1238+155C>T		intron	N/A	ENSP00000465992.1
	KIF18B	ENST00000590129.1	TSL:1	c.1265+155C>T		intron	N/A	ENSP00000465501.1
	KIF18B	ENST00000914031.1		c.1238+155C>T		intron	N/A	ENSP00000584090.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64449 AN: 151902 Hom.: 13707 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.410

GnomAD4 exome AF: 0.407 AC: 191721 AN: 470660 Hom.: 39451 Cov.: 5 AF XY: 0.406 AC XY: 100804 AN XY: 248138

African (AFR) AF: 0.484 AC: 6463 AN: 13356

American (AMR) AF: 0.382 AC: 7714 AN: 20190

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 6356 AN: 13892

East Asian (EAS) AF: 0.408 AC: 13209 AN: 32392

South Asian (SAS) AF: 0.403 AC: 19085 AN: 47370

European-Finnish (FIN) AF: 0.380 AC: 12225 AN: 32184

Middle Eastern (MID) AF: 0.404 AC: 798 AN: 1976

European-Non Finnish (NFE) AF: 0.407 AC: 115042 AN: 282492

Other (OTH) AF: 0.404 AC: 10829 AN: 26808

GnomAD4 genome AF: 0.425 AC: 64536 AN: 152022 Hom.: 13735 Cov.: 32 AF XY: 0.421 AC XY: 31318 AN XY: 74304

African (AFR) AF: 0.489 AC: 20272 AN: 41428

American (AMR) AF: 0.373 AC: 5707 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1639 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2011 AN: 5178

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4818

European-Finnish (FIN) AF: 0.395 AC: 4177 AN: 10584

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27490 AN: 67930

Other (OTH) AF: 0.408 AC: 861 AN: 2108

Alfa AF: 0.415 Hom.: 9713

Bravo AF: 0.425

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.089
DANN	Benign	0.55
PhyloP100		-1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs744281; hg19: chr17-43009886; COSMIC: COSV59277258; COSMIC: COSV59277258;