dbSNP rs211299: KIF5B:c.126+29C>T (chr10-32055819-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_004521.3(KIF5B):c.126+29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,608,032 control chromosomes in the GnomAD database, including 11,109 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 0.095 ( 794 hom., cov: 33)

Exomes 𝑓: 0.11 ( 10315 hom. )

Consequence

KIF5B
NM_004521.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0920

Publications

6 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3 link	c.126+29C>T	intron_variant	Intron 1 of 25	ENST00000302418.5	NP_004512.1	P33176V9HW29Q6P164
KIF5B	XM_047425202.1 link	c.126+29C>T	intron_variant	Intron 1 of 24		XP_047281158.1
KIF5B	XM_047425203.1 link	c.-371+29C>T	intron_variant	Intron 1 of 26		XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5 link	c.126+29C>T		intron_variant	Intron 1 of 25	1	NM_004521.3	ENSP00000307078.4		P33176

Frequencies

GnomAD3 genomes

AF:

0.0946

AC:

14384

AN:

152128

Hom.:

794

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0658

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.0615

Gnomad ASJ

AF:

0.0928

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.0870

GnomAD2 exomes

AF:

0.0991

AC:

24389

AN:

246108

AF XY:

0.106

show subpopulations

Gnomad AFR exome

AF:

0.0619

Gnomad AMR exome

AF:

0.0415

Gnomad ASJ exome

AF:

0.0949

Gnomad EAS exome

AF:

0.00120

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.112

GnomAD4 exome

AF:

0.115

AC:

166935

AN:

1455786

Hom.:

10315

Cov.:

AF XY:

0.116

AC XY:

84235

AN XY:

723862

show subpopulations

African (AFR)

AF:

0.0657

AC:

2198

AN:

33432

American (AMR)

AF:

0.0440

AC:

1964

AN:

44624

Ashkenazi Jewish (ASJ)

AF:

0.0914

AC:

2386

AN:

26102

East Asian (EAS)

AF:

0.000606

AC:

AN:

39596

South Asian (SAS)

AF:

0.137

AC:

11819

AN:

86178

European-Finnish (FIN)

AF:

0.118

AC:

5860

AN:

49786

Middle Eastern (MID)

AF:

0.149

AC:

859

AN:

5758

European-Non Finnish (NFE)

AF:

0.122

AC:

135700

AN:

1110120

Other (OTH)

AF:

0.102

AC:

6125

AN:

60190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

7468

14937

22405

29874

37342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4808

9616

14424

19232

24040

<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:

0.0945

AC:

14389

AN:

152246

Hom.:

794

Cov.:

AF XY:

0.0947

AC XY:

7049

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0658

AC:

2736

AN:

41570

American (AMR)

AF:

0.0614

AC:

940

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0928

AC:

322

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5172

South Asian (SAS)

AF:

0.120

AC:

578

AN:

4822

European-Finnish (FIN)

AF:

0.109

AC:

1156

AN:

10606

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8308

AN:

67988

Other (OTH)

AF:

0.0861

AC:

182

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

705

1410

2115

2820

3525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.106

Hom.:

314

Bravo

AF:

0.0887

Asia WGS

AF:

0.0600

AC:

209

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.4

(source)

DANN

Benign

0.91

PhyloP100

0.092

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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