Genetic Variant STK24:c.1054-60A>C (chr13-98460500-T-G) – 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.1054-60A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 1,445,150 control chromosomes in the GnomAD database, including 512,569 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 0.74 ( 43900 hom., cov: 32)

Exomes 𝑓: 0.85 ( 468669 hom. )

Consequence

STK24
NM_001032296.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.335

Publications

3 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032296.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STK24	NM_001032296.4	MANE Select	c.1054-60A>C	intron	N/A	NP_001027467.2
STK24	NM_003576.5		c.1090-60A>C	intron	N/A	NP_003567.2
STK24	NM_001286649.2		c.997-60A>C	intron	N/A	NP_001273578.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STK24	ENST00000539966.6	TSL:1 MANE Select	c.1054-60A>C	intron	N/A	ENSP00000442539.2
STK24	ENST00000376547.7	TSL:1	c.1090-60A>C	intron	N/A	ENSP00000365730.3
STK24	ENST00000444574.1	TSL:1	c.805-60A>C	intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes

AF:

0.741

AC:

112484

AN:

151844

Hom.:

43890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.496

Gnomad AMI

AF:

0.978

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.815

Gnomad EAS

AF:

0.719

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.761

GnomAD4 exome

AF:

0.846

AC:

1093699

AN:

1293188

Hom.:

468669

AF XY:

0.842

AC XY:

548272

AN XY:

650790

show subpopulations

African (AFR)

AF:

0.486

AC:

14413

AN:

29640

American (AMR)

AF:

0.568

AC:

24191

AN:

42572

Ashkenazi Jewish (ASJ)

AF:

0.820

AC:

20394

AN:

24862

East Asian (EAS)

AF:

0.742

AC:

28757

AN:

38768

South Asian (SAS)

AF:

0.683

AC:

55146

AN:

80692

European-Finnish (FIN)

AF:

0.883

AC:

46379

AN:

52548

Middle Eastern (MID)

AF:

0.753

AC:

4055

AN:

5382

European-Non Finnish (NFE)

AF:

0.887

AC:

855232

AN:

963888

Other (OTH)

AF:

0.823

AC:

45132

AN:

54836

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

7873

15745

23618

31490

39363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17420

34840

52260

69680

87100

<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:

0.741

AC:

112529

AN:

151962

Hom.:

43900

Cov.:

AF XY:

0.739

AC XY:

54881

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.496

AC:

20549

AN:

41392

American (AMR)

AF:

0.666

AC:

10177

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.815

AC:

2827

AN:

3470

East Asian (EAS)

AF:

0.719

AC:

3691

AN:

5136

South Asian (SAS)

AF:

0.662

AC:

3186

AN:

4814

European-Finnish (FIN)

AF:

0.880

AC:

9306

AN:

10576

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.884

AC:

60072

AN:

67970

Other (OTH)

AF:

0.761

AC:

1605

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1294

2588

3882

5176

6470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.759

Hom.:

21482

Bravo

AF:

0.715

Asia WGS

AF:

0.709

AC:

2466

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.95

(source)

DANN

Benign

0.46

PhyloP100

-0.34

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over