rs744281

chr17-44932518-G-Achr17-44932518-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF18B	NM_001265577.2	c.1238+155C>T		intron_variant		ENST00000593135.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF18B	ENST00000593135.6	c.1238+155C>T		intron_variant		5	NM_001265577.2	A2
KIF18B	ENST00000590129.1	c.1265+155C>T		intron_variant		1		P4
KIF18B	ENST00000587309.5	c.1238+155C>T		intron_variant		5		A2
KIF18B	ENST00000585687.1	n.385C>T		non_coding_transcript_exon_variant	3/3	3

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

Gnomad4 AFR exome AF: 0.484

Gnomad4 AMR exome AF: 0.382

Gnomad4 ASJ exome AF: 0.458

Gnomad4 EAS exome AF: 0.408

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.407

Gnomad4 OTH exome AF: 0.404

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

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.408

Alfa AF: 0.415 Hom.: 6820

Bravo AF: 0.425

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.089
Dann	Benign	0.55
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs744281; hg19: chr17-43009886; COSMIC: COSV59277258; COSMIC: COSV59277258;