rs9513431

Variant names:

• chr13-98482372-A-T
• rs9513431
• NM_001032296.4:c.274-51T>A

Variant summary

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

The NM_001032296.4(STK24):​c.274-51T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,136,156 control chromosomes in the GnomAD database, including 42,670 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 0.25 (4995 hom., cov: 32)
  • Exomes 𝑓: 0.28 (37675 hom.)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.274-51T>A		intron_variant	Intron 2 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.310-51T>A		intron_variant	Intron 2 of 10		NP_003567.2
STK24	NM_001286649.2	c.274-7014T>A		intron_variant	Intron 2 of 9		NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.274-51T>A		intron_variant	Intron 2 of 10	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38235 AN: 151902 Hom.: 4989 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.247

GnomAD3 exomes AF: 0.233 AC: 39304 AN: 168842 Hom.: 4709 AF XY: 0.235 AC XY: 21840 AN XY: 92766

Gnomad AFR exome AF: 0.199

Gnomad AMR exome AF: 0.155

Gnomad ASJ exome AF: 0.263

Gnomad EAS exome AF: 0.125

Gnomad SAS exome AF: 0.201

Gnomad FIN exome AF: 0.274

Gnomad NFE exome AF: 0.271

Gnomad OTH exome AF: 0.246

GnomAD4 exome AF: 0.275 AC: 271082 AN: 984136 Hom.: 37675 Cov.: 13 AF XY: 0.274 AC XY: 138314 AN XY: 504936

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.168

Gnomad4 ASJ exome AF: 0.274

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.276

Gnomad4 NFE exome AF: 0.296

Gnomad4 OTH exome AF: 0.268

GnomAD4 genome AF: 0.252 AC: 38259 AN: 152020 Hom.: 4995 Cov.: 32 AF XY: 0.248 AC XY: 18399 AN XY: 74316

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.250

Alfa AF: 0.271 Hom.: 1091

Bravo AF: 0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.19

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: rs9513431; hg19: chr13-99134626;