NM_001032296.4:c.330+198dupT
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1
The NM_001032296.4(STK24):c.330+198dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 99,842 control chromosomes in the GnomAD database, including 35 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.024 ( 35 hom., cov: 31)
Consequence
STK24
NM_001032296.4 intron
NM_001032296.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.87
Publications
1 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK24 | NM_001032296.4 | c.330+198dupT | intron_variant | Intron 3 of 10 | ENST00000539966.6 | NP_001027467.2 | ||
STK24 | NM_003576.5 | c.366+198dupT | intron_variant | Intron 3 of 10 | NP_003567.2 | |||
STK24 | NM_001286649.2 | c.274-6709dupT | intron_variant | Intron 2 of 9 | NP_001273578.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0235 AC: 2348AN: 99812Hom.: 32 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2348
AN:
99812
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0237 AC: 2366AN: 99842Hom.: 35 Cov.: 31 AF XY: 0.0249 AC XY: 1164AN XY: 46732 show subpopulations
GnomAD4 genome
AF:
AC:
2366
AN:
99842
Hom.:
Cov.:
31
AF XY:
AC XY:
1164
AN XY:
46732
show subpopulations
African (AFR)
AF:
AC:
1574
AN:
27222
American (AMR)
AF:
AC:
158
AN:
9478
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
2584
East Asian (EAS)
AF:
AC:
101
AN:
3402
South Asian (SAS)
AF:
AC:
30
AN:
3034
European-Finnish (FIN)
AF:
AC:
20
AN:
4536
Middle Eastern (MID)
AF:
AC:
4
AN:
144
European-Non Finnish (NFE)
AF:
AC:
434
AN:
47522
Other (OTH)
AF:
AC:
42
AN:
1336
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.490
Heterozygous variant carriers
0
107
214
322
429
536
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
28
56
84
112
140
<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:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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