GeneBe

13-98457465-CTTTTTTTTTTT-CTTTTTTT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001032296.4(STK24):​c.1123-165_1123-162delAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00035 ( 0 hom., cov: 0)

Consequence

STK24
NM_001032296.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Publications

1 publications found
Variant links:
Genes affected
STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STK24NM_001032296.4 linkc.1123-165_1123-162delAAAA intron_variant Intron 9 of 10 ENST00000539966.6 NP_001027467.2
STK24NM_003576.5 linkc.1159-165_1159-162delAAAA intron_variant Intron 9 of 10 NP_003567.2
STK24NM_001286649.2 linkc.1066-165_1066-162delAAAA intron_variant Intron 8 of 9 NP_001273578.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STK24ENST00000539966.6 linkc.1123-165_1123-162delAAAA intron_variant Intron 9 of 10 1 NM_001032296.4 ENSP00000442539.2

Frequencies

GnomAD3 genomes
AF:
0.000352
AC:
39
AN:
110790
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000852
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000187
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000253
Gnomad SAS
AF:
0.000573
Gnomad FIN
AF:
0.000770
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000111
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.000352
AC:
39
AN:
110792
Hom.:
0
Cov.:
0
AF XY:
0.000504
AC XY:
26
AN XY:
51622
show subpopulations
African (AFR)
AF:
0.000851
AC:
25
AN:
29382
American (AMR)
AF:
0.000187
AC:
2
AN:
10696
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2926
East Asian (EAS)
AF:
0.000254
AC:
1
AN:
3936
South Asian (SAS)
AF:
0.000577
AC:
2
AN:
3466
European-Finnish (FIN)
AF:
0.000770
AC:
3
AN:
3898
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
222
European-Non Finnish (NFE)
AF:
0.000111
AC:
6
AN:
54128
Other (OTH)
AF:
0.00
AC:
0
AN:
1466
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.479
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.010
Mutation Taster
=99/1
polymorphism

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: rs11351684; hg19: chr13-99109719; COSMIC: COSV104427716; COSMIC: COSV104427716; API