NM_194313.4:c.1215+1671C>T

Variant summary

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

The NM_194313.4(KIF24):​c.1215+1671C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,012 control chromosomes in the GnomAD database, including 10,858 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 0.35 ( 10858 hom., cov: 31)

Consequence

KIF24
NM_194313.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0790

Publications

6 publications found
Variant links:
Genes affected
KIF24 (HGNC:19916): (kinesin family member 24) This gene encodes a member of the kinesin superfamily of microtubule-based motor proteins which are involved in the intracellular transport of membranous organelles, protein complexes, and mRNAs. They also play critical roles in mitosis, morphogenesis, and signal transduction. The encoded protein contains an N-terminal sterile alpha motif (SAM) domain and an ATP-binding kinesin motor domain. It binds centriolar coiled coil protein 110 and centrosomal protein 97 and localizes to the mother centriole to regulate ciliogenesis by controlling microtubule polymerization. [provided by RefSeq, Mar 2017]
KIF24 Gene-Disease associations (from GenCC):
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

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=-0.75).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIF24NM_194313.4 linkc.1215+1671C>T intron_variant Intron 6 of 12 ENST00000402558.7 NP_919289.2 Q5T7B8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIF24ENST00000402558.7 linkc.1215+1671C>T intron_variant Intron 6 of 12 5 NM_194313.4 ENSP00000384433.1 Q5T7B8-1
KIF24ENST00000379174.7 linkc.814-13016C>T intron_variant Intron 2 of 8 5 ENSP00000368472.3 Q5T7B8-2

Frequencies

GnomAD3 genomes
AF:
0.352
AC:
53455
AN:
151894
Hom.:
10853
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.527
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.354
Gnomad SAS
AF:
0.575
Gnomad FIN
AF:
0.388
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.452
Gnomad OTH
AF:
0.383
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.352
AC:
53467
AN:
152012
Hom.:
10858
Cov.:
31
AF XY:
0.354
AC XY:
26313
AN XY:
74294
show subpopulations
African (AFR)
AF:
0.140
AC:
5800
AN:
41490
American (AMR)
AF:
0.353
AC:
5394
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.418
AC:
1451
AN:
3470
East Asian (EAS)
AF:
0.354
AC:
1831
AN:
5170
South Asian (SAS)
AF:
0.576
AC:
2770
AN:
4806
European-Finnish (FIN)
AF:
0.388
AC:
4093
AN:
10542
Middle Eastern (MID)
AF:
0.435
AC:
128
AN:
294
European-Non Finnish (NFE)
AF:
0.452
AC:
30708
AN:
67960
Other (OTH)
AF:
0.385
AC:
811
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1642
3284
4925
6567
8209
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
536
1072
1608
2144
2680
<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:
0.423
Hom.:
15446
Bravo
AF:
0.336
Asia WGS
AF:
0.456
AC:
1585
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
4.6
DANN
Benign
0.84
PhyloP100
-0.079
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs17350373; hg19: chr9-34284944; API