Genetic Variant STK24:c.783+40G>A (chr13-98466336-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001032296.4(STK24):c.783+40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 1,589,048 control chromosomes in the GnomAD database, including 60,622 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 0.25 ( 4986 hom., cov: 33)

Exomes 𝑓: 0.28 ( 55636 hom. )

Consequence

STK24
NM_001032296.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0990

Publications

5 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]

STK24 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4 link	c.783+40G>A	intron_variant	Intron 6 of 10	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
STK24	NM_003576.5 link	c.819+40G>A	intron_variant	Intron 6 of 10		NP_003567.2	Q9Y6E0-1
STK24	NM_001286649.2 link	c.726+40G>A	intron_variant	Intron 5 of 9		NP_001273578.1	B4DR80

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6 link	c.783+40G>A		intron_variant	Intron 6 of 10	1	NM_001032296.4	ENSP00000442539.2		Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38398

AN:

152002

Hom.:

4978

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.248

GnomAD2 exomes

AF:

0.251

AC:

59988

AN:

239066

AF XY:

0.253

show subpopulations

Gnomad AFR exome

AF:

0.211

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.251

Gnomad EAS exome

AF:

0.172

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.245

GnomAD4 exome

AF:

0.276

AC:

396165

AN:

1436928

Hom.:

55636

Cov.:

AF XY:

0.275

AC XY:

195902

AN XY:

712828

show subpopulations

African (AFR)

AF:

0.204

AC:

6669

AN:

32668

American (AMR)

AF:

0.221

AC:

9333

AN:

42274

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

6431

AN:

25350

East Asian (EAS)

AF:

0.172

AC:

6766

AN:

39356

South Asian (SAS)

AF:

0.232

AC:

19352

AN:

83510

European-Finnish (FIN)

AF:

0.245

AC:

12959

AN:

52866

Middle Eastern (MID)

AF:

0.217

AC:

880

AN:

4046

European-Non Finnish (NFE)

AF:

0.290

AC:

318375

AN:

1097672

Other (OTH)

AF:

0.260

AC:

15400

AN:

59186

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

14459

28919

43378

57838

72297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10488

20976

31464

41952

52440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.253

AC:

38430

AN:

152120

Hom.:

4986

Cov.:

AF XY:

0.249

AC XY:

18499

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.211

AC:

8750

AN:

41494

American (AMR)

AF:

0.241

AC:

3691

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

871

AN:

3472

East Asian (EAS)

AF:

0.165

AC:

853

AN:

5170

South Asian (SAS)

AF:

0.214

AC:

1034

AN:

4824

European-Finnish (FIN)

AF:

0.226

AC:

2389

AN:

10578

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.295

AC:

20032

AN:

67976

Other (OTH)

AF:

0.248

AC:

523

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1505

3010

4515

6020

7525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.272

Hom.:

13600

Bravo

AF:

0.249

Asia WGS

AF:

0.195

AC:

678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.8

(source)

DANN

Benign

0.44

PhyloP100

0.099

PromoterAI

-0.024

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over