Variant chr13-98475242-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001032296.4(STK24):c.439+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,596,924 control chromosomes in the GnomAD database, including 65,862 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 6545 hom., cov: 32)

Exomes 𝑓: 0.28 ( 59317 hom. )

Consequence

STK24
NM_001032296.4 splice_region, intron

Scores

Splicing: ADA: 0.00006093

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0810

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
STK24	NM_001032296.4 linkuse as main transcript	c.439+8G>A	splice_region_variant, intron_variant	ENST00000539966.6
STK24	NM_001286649.2 linkuse as main transcript	c.382+8G>A	splice_region_variant, intron_variant
STK24	NM_003576.5 linkuse as main transcript	c.475+8G>A	splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6 linkuse as main transcript	c.439+8G>A		splice_region_variant, intron_variant		1	NM_001032296.4	P1	Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.289

AC:

43963

AN:

151978

Hom.:

6540

Cov.:

show subpopulations

Gnomad AFR

AF:

0.337

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.280

GnomAD3 exomes

AF:

0.257

AC:

62874

AN:

244930

Hom.:

8566

AF XY:

0.257

AC XY:

34051

AN XY:

132254

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.167

Gnomad ASJ exome

AF:

0.282

Gnomad EAS exome

AF:

0.140

Gnomad SAS exome

AF:

0.216

Gnomad FIN exome

AF:

0.282

Gnomad NFE exome

AF:

0.293

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.283

AC:

409294

AN:

1444828

Hom.:

59317

Cov.:

AF XY:

0.282

AC XY:

202619

AN XY:

719412

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.176

Gnomad4 ASJ exome

AF:

0.276

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.278

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.281

GnomAD4 genome

AF:

0.289

AC:

43996

AN:

152096

Hom.:

6545

Cov.:

AF XY:

0.283

AC XY:

21077

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.337

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.219

Gnomad4 FIN

AF:

0.272

Gnomad4 NFE

AF:

0.297

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.293

Hom.:

4905

Bravo

AF:

0.286

Asia WGS

AF:

0.197

AC:

684

AN:

3478

EpiCase

AF:

0.292

EpiControl

AF:

0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.82

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000061

dbscSNV1_RF

Benign

0.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over