Genetic Variant KIF5B:c.1374+139G>A (chr10-32032567-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004521.3(KIF5B):c.1374+139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 674,742 control chromosomes in the GnomAD database, including 17,201 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 0.21 ( 3616 hom., cov: 32)

Exomes 𝑓: 0.22 ( 13585 hom. )

Consequence

KIF5B
NM_004521.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106

Publications

3 publications found

Variant links:

Genes affected

KIF5B (HGNC:6324): (kinesin family member 5B) Enables identical protein binding activity; microtubule binding activity; and microtubule motor activity. Involved in several processes, including lysosome localization; natural killer cell mediated cytotoxicity; and positive regulation of protein localization to plasma membrane. Located in centriolar satellite; cytosol; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

KIF5B 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3 link	c.1374+139G>A	intron_variant	Intron 13 of 25	ENST00000302418.5	NP_004512.1	P33176V9HW29Q6P164
KIF5B	XM_047425202.1 link	c.1374+139G>A	intron_variant	Intron 13 of 24		XP_047281158.1
KIF5B	XM_047425203.1 link	c.1092+139G>A	intron_variant	Intron 14 of 26		XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5 link	c.1374+139G>A		intron_variant	Intron 13 of 25	1	NM_004521.3	ENSP00000307078.4		P33176

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32230

AN:

151966

Hom.:

3607

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.00789

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.211

GnomAD4 exome

AF:

0.216

AC:

113092

AN:

522658

Hom.:

13585

AF XY:

0.217

AC XY:

60792

AN XY:

279910

show subpopulations

African (AFR)

AF:

0.201

AC:

2772

AN:

13810

American (AMR)

AF:

0.197

AC:

4929

AN:

25074

Ashkenazi Jewish (ASJ)

AF:

0.232

AC:

3664

AN:

15800

East Asian (EAS)

AF:

0.00469

AC:

152

AN:

32420

South Asian (SAS)

AF:

0.201

AC:

10460

AN:

52000

European-Finnish (FIN)

AF:

0.190

AC:

8654

AN:

45582

Middle Eastern (MID)

AF:

0.280

AC:

895

AN:

3202

European-Non Finnish (NFE)

AF:

0.246

AC:

75443

AN:

306270

Other (OTH)

AF:

0.215

AC:

6123

AN:

28500

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

4074

8148

12221

16295

20369

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.212

AC:

32277

AN:

152084

Hom.:

3616

Cov.:

AF XY:

0.208

AC XY:

15439

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.203

AC:

8412

AN:

41496

American (AMR)

AF:

0.187

AC:

2851

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

813

AN:

3470

East Asian (EAS)

AF:

0.00772

AC:

AN:

5182

South Asian (SAS)

AF:

0.178

AC:

860

AN:

4826

European-Finnish (FIN)

AF:

0.183

AC:

1934

AN:

10556

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.245

AC:

16684

AN:

67962

Other (OTH)

AF:

0.214

AC:

452

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1301

2602

3904

5205

6506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.226

Hom.:

495

Bravo

AF:

0.214

Asia WGS

AF:

0.130

AC:

451

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.91

(source)

DANN

Benign

0.40

PhyloP100

-0.11

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