dbSNP rs2031237: STK24:c.1259+103G>T (chr13-98457065-C-A) – 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.1259+103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 1,398,436 control chromosomes in the GnomAD database, including 54,866 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 0.26 ( 5223 hom., cov: 33)

Exomes 𝑓: 0.28 ( 49643 hom. )

Consequence

STK24
NM_001032296.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409

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:

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4 link	c.1259+103G>T	intron_variant	Intron 10 of 10	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
STK24	NM_003576.5 link	c.1295+103G>T	intron_variant	Intron 10 of 10		NP_003567.2	Q9Y6E0-1
STK24	NM_001286649.2 link	c.1202+103G>T	intron_variant	Intron 9 of 9		NP_001273578.1	B4DR80

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6 link	c.1259+103G>T		intron_variant	Intron 10 of 10	1	NM_001032296.4	ENSP00000442539.2		Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39237

AN:

151982

Hom.:

5209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.252

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.258

GnomAD4 exome

AF:

0.279

AC:

347529

AN:

1246334

Hom.:

49643

Cov.:

AF XY:

0.278

AC XY:

170037

AN XY:

612578

show subpopulations

African (AFR)

AF:

0.224

AC:

6172

AN:

27530

American (AMR)

AF:

0.223

AC:

5563

AN:

24974

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

5340

AN:

20390

East Asian (EAS)

AF:

0.144

AC:

5093

AN:

35426

South Asian (SAS)

AF:

0.229

AC:

15527

AN:

67754

European-Finnish (FIN)

AF:

0.249

AC:

9096

AN:

36470

Middle Eastern (MID)

AF:

0.219

AC:

791

AN:

3614

European-Non Finnish (NFE)

AF:

0.293

AC:

286143

AN:

977646

Other (OTH)

AF:

0.263

AC:

13804

AN:

52530

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

12021

24042

36064

48085

60106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9478

18956

28434

37912

47390

<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:

0.258

AC:

39282

AN:

152102

Hom.:

5223

Cov.:

AF XY:

0.254

AC XY:

18851

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.228

AC:

9462

AN:

41490

American (AMR)

AF:

0.241

AC:

3692

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

891

AN:

3472

East Asian (EAS)

AF:

0.154

AC:

798

AN:

5166

South Asian (SAS)

AF:

0.213

AC:

1030

AN:

4828

European-Finnish (FIN)

AF:

0.226

AC:

2385

AN:

10570

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20121

AN:

67968

Other (OTH)

AF:

0.257

AC:

543

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1499

2998

4498

5997

7496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.418

Hom.:

3246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.4

(source)

DANN

Benign

0.46

PhyloP100

-0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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