Genetic Variant STK24:c.1259+103G>A (chr13-98457065-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.1259+103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,398,502 control chromosomes in the GnomAD database, including 31,989 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 0.22 ( 3738 hom., cov: 33)

Exomes 𝑓: 0.21 ( 28251 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:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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.1259+103G>A	intron	N/A	NP_001027467.2
STK24	NM_003576.5		c.1295+103G>A	intron	N/A	NP_003567.2
STK24	NM_001286649.2		c.1202+103G>A	intron	N/A	NP_001273578.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
STK24	ENST00000539966.6	TSL:1 MANE Select	c.1259+103G>A	intron	N/A	ENSP00000442539.2
STK24	ENST00000376547.7	TSL:1	c.1295+103G>A	intron	N/A	ENSP00000365730.3
STK24	ENST00000444574.1	TSL:1	c.1010+103G>A	intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33066

AN:

151986

Hom.:

3732

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.252

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.211

AC:

262605

AN:

1246396

Hom.:

28251

Cov.:

AF XY:

0.211

AC XY:

129480

AN XY:

612664

show subpopulations

African (AFR)

AF:

0.261

AC:

7176

AN:

27522

American (AMR)

AF:

0.160

AC:

4006

AN:

24982

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

4498

AN:

20392

East Asian (EAS)

AF:

0.118

AC:

4190

AN:

35442

South Asian (SAS)

AF:

0.216

AC:

14625

AN:

67752

European-Finnish (FIN)

AF:

0.174

AC:

6347

AN:

36474

Middle Eastern (MID)

AF:

0.250

AC:

903

AN:

3616

European-Non Finnish (NFE)

AF:

0.214

AC:

209481

AN:

977700

Other (OTH)

AF:

0.217

AC:

11379

AN:

52516

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

10025

20050

30074

40099

50124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7306

14612

21918

29224

36530

<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:

0.218

AC:

33095

AN:

152106

Hom.:

3738

Cov.:

AF XY:

0.213

AC XY:

15864

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.255

AC:

10566

AN:

41476

American (AMR)

AF:

0.183

AC:

2796

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

814

AN:

3472

East Asian (EAS)

AF:

0.142

AC:

735

AN:

5170

South Asian (SAS)

AF:

0.211

AC:

1019

AN:

4822

European-Finnish (FIN)

AF:

0.167

AC:

1768

AN:

10568

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14698

AN:

67984

Other (OTH)

AF:

0.223

AC:

471

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1325

2649

3974

5298

6623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.0297

Hom.:

3246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.3

(source)

DANN

Benign

0.34

PhyloP100

-0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

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