NM_001032296.4:c.330+3225G>A

Variant summary

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

The NM_001032296.4(STK24):​c.330+3225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,144 control chromosomes in the GnomAD database, including 6,125 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 0.27 ( 6125 hom., cov: 32)

Consequence

STK24
NM_001032296.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STK24NM_001032296.4 linkc.330+3225G>A intron_variant Intron 3 of 10 ENST00000539966.6 NP_001027467.2 Q9Y6E0-2Q5U0E6Q6P0Y1
STK24NM_003576.5 linkc.366+3225G>A intron_variant Intron 3 of 10 NP_003567.2 Q9Y6E0-1
STK24NM_001286649.2 linkc.274-3682G>A 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+3225G>A intron_variant Intron 3 of 10 1 NM_001032296.4 ENSP00000442539.2 Q9Y6E0-2

Frequencies

GnomAD3 genomes
AF:
0.268
AC:
40777
AN:
152026
Hom.:
6127
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.135
Gnomad AMI
AF:
0.531
Gnomad AMR
AF:
0.248
Gnomad ASJ
AF:
0.265
Gnomad EAS
AF:
0.416
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.322
Gnomad OTH
AF:
0.272
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.268
AC:
40765
AN:
152144
Hom.:
6125
Cov.:
32
AF XY:
0.272
AC XY:
20252
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.135
Gnomad4 AMR
AF:
0.247
Gnomad4 ASJ
AF:
0.265
Gnomad4 EAS
AF:
0.415
Gnomad4 SAS
AF:
0.227
Gnomad4 FIN
AF:
0.396
Gnomad4 NFE
AF:
0.322
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.300
Hom.:
7163
Bravo
AF:
0.256
Asia WGS
AF:
0.305
AC:
1059
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.73
DANN
Benign
0.74

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: rs912330; hg19: chr13-99131294; API