NM_001032296.4:c.330+198dupT

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.87

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: 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
STK24NM_001032296.4 linkc.330+198dupT intron_variant Intron 3 of 10 ENST00000539966.6 NP_001027467.2 Q9Y6E0-2Q5U0E6Q6P0Y1
STK24NM_003576.5 linkc.366+198dupT intron_variant Intron 3 of 10 NP_003567.2 Q9Y6E0-1
STK24NM_001286649.2 linkc.274-6709dupT intron_variant Intron 2 of 9 NP_001273578.1 B4DR80

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STK24ENST00000539966.6 linkc.330+198_330+199insT intron_variant Intron 3 of 10 1 NM_001032296.4 ENSP00000442539.2 Q9Y6E0-2

Frequencies

GnomAD3 genomes
AF:
0.0235
AC:
2348
AN:
99812
Hom.:
32
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0574
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0163
Gnomad ASJ
AF:
0.00116
Gnomad EAS
AF:
0.0296
Gnomad SAS
AF:
0.0102
Gnomad FIN
AF:
0.00441
Gnomad MID
AF:
0.0247
Gnomad NFE
AF:
0.00913
Gnomad OTH
AF:
0.0316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0237
AC:
2366
AN:
99842
Hom.:
35
Cov.:
31
AF XY:
0.0249
AC XY:
1164
AN XY:
46732
show subpopulations
African (AFR)
AF:
0.0578
AC:
1574
AN:
27222
American (AMR)
AF:
0.0167
AC:
158
AN:
9478
Ashkenazi Jewish (ASJ)
AF:
0.00116
AC:
3
AN:
2584
East Asian (EAS)
AF:
0.0297
AC:
101
AN:
3402
South Asian (SAS)
AF:
0.00989
AC:
30
AN:
3034
European-Finnish (FIN)
AF:
0.00441
AC:
20
AN:
4536
Middle Eastern (MID)
AF:
0.0278
AC:
4
AN:
144
European-Non Finnish (NFE)
AF:
0.00913
AC:
434
AN:
47522
Other (OTH)
AF:
0.0314
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:
0.000769
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.9
Mutation Taster
=100/0
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: rs34520150; hg19: chr13-99134320; API