rs12682543

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015254.4(KIF13B):​c.149+23305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,764 control chromosomes in the GnomAD database, including 24,724 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 0.54 ( 24724 hom., cov: 31)

Consequence

KIF13B
NM_015254.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.820
Variant links:
Genes affected
KIF13B (HGNC:14405): (kinesin family member 13B) Enables 14-3-3 protein binding activity and protein kinase binding activity. Involved in regulation of axonogenesis. Located in axon and cytoplasm. [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=-1.0).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF13BNM_015254.4 linkuse as main transcriptc.149+23305C>T intron_variant ENST00000524189.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF13BENST00000524189.6 linkuse as main transcriptc.149+23305C>T intron_variant 1 NM_015254.4 P1Q9NQT8-1

Frequencies

GnomAD3 genomes
AF:
0.545
AC:
82647
AN:
151650
Hom.:
24723
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.302
Gnomad AMI
AF:
0.712
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.582
Gnomad EAS
AF:
0.337
Gnomad SAS
AF:
0.587
Gnomad FIN
AF:
0.605
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.678
Gnomad OTH
AF:
0.585
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.545
AC:
82667
AN:
151764
Hom.:
24724
Cov.:
31
AF XY:
0.541
AC XY:
40123
AN XY:
74144
show subpopulations
Gnomad4 AFR
AF:
0.302
Gnomad4 AMR
AF:
0.594
Gnomad4 ASJ
AF:
0.582
Gnomad4 EAS
AF:
0.338
Gnomad4 SAS
AF:
0.587
Gnomad4 FIN
AF:
0.605
Gnomad4 NFE
AF:
0.678
Gnomad4 OTH
AF:
0.578
Alfa
AF:
0.650
Hom.:
33884
Bravo
AF:
0.533
Asia WGS
AF:
0.434
AC:
1509
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.0
DANN
Benign
0.59

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: rs12682543; hg19: chr8-29079558; API