NM_013233.3:c.1090-24281T>C

Variant names:

• chr2-168099512-A-G
• rs6745588
• NM_013233.3:c.1090-24281T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013233.3(STK39):​c.1090-24281T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,048 control chromosomes in the GnomAD database, including 10,283 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 0.36 (10283 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 3 publications found

Genes affected

STK39 (HGNC:17717): (serine/threonine kinase 39) This gene encodes a serine/threonine kinase that is thought to function in the cellular stress response pathway. The kinase is activated in response to hypotonic stress, leading to phosphorylation of several cation-chloride-coupled cotransporters. The catalytically active kinase specifically activates the p38 MAP kinase pathway, and its interaction with p38 decreases upon cellular stress, suggesting that this kinase may serve as an intermediate in the response to cellular stress. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.1090-24281T>C		intron_variant	Intron 10 of 17	ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.1090-24281T>C		intron_variant	Intron 10 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000487143.5	n.189+13406T>C		intron_variant	Intron 1 of 8	1
STK39	ENST00000697205.1	c.1090-24281T>C		intron_variant	Intron 10 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54720 AN: 151930 Hom.: 10278 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.325

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.360 AC: 54774 AN: 152048 Hom.: 10283 Cov.: 32 AF XY: 0.362 AC XY: 26914 AN XY: 74344

African (AFR) AF: 0.426 AC: 17661 AN: 41432

American (AMR) AF: 0.392 AC: 5997 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3470

East Asian (EAS) AF: 0.162 AC: 839 AN: 5174

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4814

European-Finnish (FIN) AF: 0.406 AC: 4290 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22599 AN: 67980

Other (OTH) AF: 0.326 AC: 689 AN: 2114

Alfa AF: 0.339 Hom.: 6728

Bravo AF: 0.363

Asia WGS AF: 0.243 AC: 847 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.4
DANN	Benign	0.82
PhyloP100		1.0
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: rs6745588; hg19: chr2-168956022;