rs398686

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 HGVSp Effect #exon/exons MANE Protein UniProt
KIF5BNM_004521.3 linkuse as main transcriptc.1374+139G>A intron_variant ENST00000302418.5 NP_004512.1
KIF5BXM_047425202.1 linkuse as main transcriptc.1374+139G>A intron_variant XP_047281158.1
KIF5BXM_047425203.1 linkuse as main transcriptc.1092+139G>A intron_variant XP_047281159.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF5BENST00000302418.5 linkuse as main transcriptc.1374+139G>A intron_variant 1 NM_004521.3 ENSP00000307078 P1

Frequencies

GnomAD3 genomes
AF:
0.212
AC:
32230
AN:
151966
Hom.:
3607
Cov.:
32
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
Gnomad4 AFR exome
AF:
0.201
Gnomad4 AMR exome
AF:
0.197
Gnomad4 ASJ exome
AF:
0.232
Gnomad4 EAS exome
AF:
0.00469
Gnomad4 SAS exome
AF:
0.201
Gnomad4 FIN exome
AF:
0.190
Gnomad4 NFE exome
AF:
0.246
Gnomad4 OTH exome
AF:
0.215
GnomAD4 genome
AF:
0.212
AC:
32277
AN:
152084
Hom.:
3616
Cov.:
32
AF XY:
0.208
AC XY:
15439
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.187
Gnomad4 ASJ
AF:
0.234
Gnomad4 EAS
AF:
0.00772
Gnomad4 SAS
AF:
0.178
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.245
Gnomad4 OTH
AF:
0.214
Alfa
AF:
0.227
Hom.:
476
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
DANN
Benign
0.40

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs398686; hg19: chr10-32321495; API