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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF18B	NM_001265577.2 link	c.1238+155C>T		intron_variant	Intron 9 of 15	ENST00000593135.6	NP_001252506.1	Q86Y91-5Q6NWY8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIF18B	ENST00000593135.6 link	c.1238+155C>T	intron_variant	Intron 9 of 15	5	NM_001265577.2	ENSP00000465992.1	Q86Y91-5
KIF18B	ENST00000590129.1 link	c.1265+155C>T	intron_variant	Intron 8 of 13	1		ENSP00000465501.1	A0A494BYR6
KIF18B	ENST00000585687.1 link	n.385C>T	non_coding_transcript_exon_variant	Exon 3 of 3	3
KIF18B	ENST00000587309.5 link	c.1238+155C>T	intron_variant	Intron 9 of 14	5		ENSP00000465377.1	Q86Y91-6

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over