dbSNP rs744281: KIF18B:c.1238+155C>T (chr17-44932518-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Publications

6 publications found

Variant links:

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]

KIF18B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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	Q86Y91-5
	KIF18B	NM_001264573.2		c.1238+155C>T		intron	N/A	NP_001251503.1	Q86Y91-6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIF18B	ENST00000593135.6	TSL:5 MANE Select	c.1238+155C>T	intron	N/A	ENSP00000465992.1	Q86Y91-5
KIF18B	ENST00000590129.1	TSL:1	c.1265+155C>T	intron	N/A	ENSP00000465501.1	A0A494BYR6
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.:

show subpopulations

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.:

AF XY:

0.406

AC XY:

100804

AN XY:

248138

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

5715

11430

17145

22860

28575

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

782

1564

2346

3128

3910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.425

AC:

64536

AN:

152022

Hom.:

13735

Cov.:

AF XY:

0.421

AC XY:

31318

AN XY:

74304

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1967

3934

5900

7867

9834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over