chr13-98474998-C-G

Variant summary

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

The NM_001032296.4(STK24):​c.440-20G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 1,597,190 control chromosomes in the GnomAD database, including 245,794 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 0.54 ( 22189 hom., cov: 32)
Exomes 𝑓: 0.55 ( 223605 hom. )

Consequence

STK24
NM_001032296.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.44
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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
STK24NM_001032296.4 linkc.440-20G>C intron_variant Intron 4 of 10 ENST00000539966.6 NP_001027467.2 Q9Y6E0-2Q5U0E6Q6P0Y1
STK24NM_003576.5 linkc.476-20G>C intron_variant Intron 4 of 10 NP_003567.2 Q9Y6E0-1
STK24NM_001286649.2 linkc.383-20G>C intron_variant Intron 3 of 9 NP_001273578.1 B4DR80

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
STK24ENST00000539966.6 linkc.440-20G>C intron_variant Intron 4 of 10 1 NM_001032296.4 ENSP00000442539.2 Q9Y6E0-2

Frequencies

GnomAD3 genomes
AF:
0.536
AC:
81414
AN:
152028
Hom.:
22167
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.544
Gnomad AMI
AF:
0.433
Gnomad AMR
AF:
0.456
Gnomad ASJ
AF:
0.529
Gnomad EAS
AF:
0.296
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.494
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.582
Gnomad OTH
AF:
0.520
GnomAD3 exomes
AF:
0.507
AC:
119079
AN:
235096
Hom.:
31000
AF XY:
0.510
AC XY:
64720
AN XY:
126942
show subpopulations
Gnomad AFR exome
AF:
0.547
Gnomad AMR exome
AF:
0.390
Gnomad ASJ exome
AF:
0.535
Gnomad EAS exome
AF:
0.311
Gnomad SAS exome
AF:
0.459
Gnomad FIN exome
AF:
0.520
Gnomad NFE exome
AF:
0.576
Gnomad OTH exome
AF:
0.512
GnomAD4 exome
AF:
0.552
AC:
797757
AN:
1445044
Hom.:
223605
Cov.:
52
AF XY:
0.550
AC XY:
395056
AN XY:
717910
show subpopulations
Gnomad4 AFR exome
AF:
0.545
Gnomad4 AMR exome
AF:
0.397
Gnomad4 ASJ exome
AF:
0.523
Gnomad4 EAS exome
AF:
0.286
Gnomad4 SAS exome
AF:
0.458
Gnomad4 FIN exome
AF:
0.521
Gnomad4 NFE exome
AF:
0.578
Gnomad4 OTH exome
AF:
0.536
GnomAD4 genome
AF:
0.536
AC:
81482
AN:
152146
Hom.:
22189
Cov.:
32
AF XY:
0.526
AC XY:
39149
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.544
Gnomad4 AMR
AF:
0.456
Gnomad4 ASJ
AF:
0.529
Gnomad4 EAS
AF:
0.297
Gnomad4 SAS
AF:
0.439
Gnomad4 FIN
AF:
0.494
Gnomad4 NFE
AF:
0.582
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.511
Hom.:
2878
Bravo
AF:
0.528
Asia WGS
AF:
0.393
AC:
1366
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.015
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs9513430; hg19: chr13-99127252; COSMIC: COSV64823329; API