dbSNP rs9513431: STK24:c.274-51T>A (chr13-98482372-A-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.274-51T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,136,156 control chromosomes in the GnomAD database, including 42,670 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 ( 4995 hom., cov: 32)

Exomes 𝑓: 0.28 ( 37675 hom. )

Consequence

STK24
NM_001032296.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.327

Publications

2 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:

Genome browser will be placed here

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 = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4 link	c.274-51T>A	intron_variant	Intron 2 of 10	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
STK24	NM_003576.5 link	c.310-51T>A	intron_variant	Intron 2 of 10		NP_003567.2	Q9Y6E0-1
STK24	NM_001286649.2 link	c.274-7014T>A	intron_variant	Intron 2 of 9		NP_001273578.1	B4DR80

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6 link	c.274-51T>A		intron_variant	Intron 2 of 10	1	NM_001032296.4	ENSP00000442539.2		Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38235

AN:

151902

Hom.:

4989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.217

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.247

GnomAD2 exomes

AF:

0.233

AC:

39304

AN:

168842

AF XY:

0.235

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.263

Gnomad EAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.271

Gnomad OTH exome

AF:

0.246

GnomAD4 exome

AF:

0.275

AC:

271082

AN:

984136

Hom.:

37675

Cov.:

AF XY:

0.274

AC XY:

138314

AN XY:

504936

show subpopulations

African (AFR)

AF:

0.220

AC:

4649

AN:

21180

American (AMR)

AF:

0.168

AC:

4795

AN:

28474

Ashkenazi Jewish (ASJ)

AF:

0.274

AC:

5486

AN:

20046

East Asian (EAS)

AF:

0.112

AC:

4069

AN:

36280

South Asian (SAS)

AF:

0.213

AC:

14431

AN:

67660

European-Finnish (FIN)

AF:

0.276

AC:

13856

AN:

50232

Middle Eastern (MID)

AF:

0.279

AC:

1073

AN:

3840

European-Non Finnish (NFE)

AF:

0.296

AC:

211043

AN:

712922

Other (OTH)

AF:

0.268

AC:

11680

AN:

43502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

9168

18337

27505

36674

45842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5818

11636

17454

23272

29090

<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:

0.252

AC:

38259

AN:

152020

Hom.:

4995

Cov.:

AF XY:

0.248

AC XY:

18399

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.215

AC:

8923

AN:

41442

American (AMR)

AF:

0.198

AC:

3028

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

995

AN:

3464

East Asian (EAS)

AF:

0.131

AC:

680

AN:

5172

South Asian (SAS)

AF:

0.216

AC:

1041

AN:

4822

European-Finnish (FIN)

AF:

0.271

AC:

2866

AN:

10576

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19943

AN:

67962

Other (OTH)

AF:

0.250

AC:

526

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1432

2865

4297

5730

7162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

408

816

1224

1632

2040

<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:

0.271

Hom.:

1091

Bravo

AF:

0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.32

(source)

DANN

Benign

0.19

PhyloP100

-0.33

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