rs9582232

Positions:

• chr13-98474798-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001032296.4(STK24):​c.597+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,593,352 control chromosomes in the GnomAD database, including 27,962 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 0.16 (2019 hom., cov: 32)
  • Exomes 𝑓: 0.19 (25943 hom.)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK24	NM_001032296.4	c.597+23G>A		intron_variant		ENST00000539966.6
STK24	NM_001286649.2	c.540+23G>A		intron_variant
STK24	NM_003576.5	c.633+23G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6	c.597+23G>A		intron_variant		1	NM_001032296.4	P1
STK24	ENST00000376547.7	c.633+23G>A		intron_variant		1
STK24	ENST00000444574.1	c.349+23G>A		intron_variant		1
STK24	ENST00000397517.6	c.540+23G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23823 AN: 152086 Hom.: 2015 Cov.: 32

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.174

GnomAD3 exomes AF: 0.167 AC: 39040 AN: 234254 Hom.: 3409 AF XY: 0.170 AC XY: 21403 AN XY: 126234

Gnomad AFR exome AF: 0.0950

Gnomad AMR exome AF: 0.120

Gnomad ASJ exome AF: 0.224

Gnomad EAS exome AF: 0.137

Gnomad SAS exome AF: 0.157

Gnomad FIN exome AF: 0.168

Gnomad NFE exome AF: 0.194

Gnomad OTH exome AF: 0.177

GnomAD4 exome AF: 0.187 AC: 269628 AN: 1441148 Hom.: 25943 Cov.: 31 AF XY: 0.187 AC XY: 133501 AN XY: 715462

Gnomad4 AFR exome AF: 0.0932

Gnomad4 AMR exome AF: 0.124

Gnomad4 ASJ exome AF: 0.216

Gnomad4 EAS exome AF: 0.114

Gnomad4 SAS exome AF: 0.160

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.197

Gnomad4 OTH exome AF: 0.185

GnomAD4 genome AF: 0.157 AC: 23835 AN: 152204 Hom.: 2019 Cov.: 32 AF XY: 0.154 AC XY: 11477 AN XY: 74406

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.177

Alfa AF: 0.184 Hom.: 528

Bravo AF: 0.154

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.33
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs9582232; hg19: chr13-99127052; COSMIC: COSV64823703; COSMIC: COSV64823703;