rs9513431

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.274-51T>A		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.310-51T>A		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.274-7014T>A		intron	N/A	NP_001273578.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.274-51T>A		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.310-51T>A		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.25-51T>A		intron	N/A	ENSP00000402764.1

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

GnomAD2 exomes AF: 0.233 AC: 39304 AN: 168842 AF XY: 0.235

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 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

African (AFR) AF: 0.220 AC: 4649 AN: 21180

American (AMR) AF: 0.168 AC: 4795 AN: 28474

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 5486 AN: 20046

East Asian (EAS) AF: 0.112 AC: 4069 AN: 36280

South Asian (SAS) AF: 0.213 AC: 14431 AN: 67660

European-Finnish (FIN) AF: 0.276 AC: 13856 AN: 50232

Middle Eastern (MID) AF: 0.279 AC: 1073 AN: 3840

European-Non Finnish (NFE) AF: 0.296 AC: 211043 AN: 712922

Other (OTH) AF: 0.268 AC: 11680 AN: 43502

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

African (AFR) AF: 0.215 AC: 8923 AN: 41442

American (AMR) AF: 0.198 AC: 3028 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3464

East Asian (EAS) AF: 0.131 AC: 680 AN: 5172

South Asian (SAS) AF: 0.216 AC: 1041 AN: 4822

European-Finnish (FIN) AF: 0.271 AC: 2866 AN: 10576

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19943 AN: 67962

Other (OTH) AF: 0.250 AC: 526 AN: 2106

Alfa AF: 0.271 Hom.: 1091

Bravo AF: 0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.19
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9513431; hg19: chr13-99134626;