rs1517342

Variant names:

• chr2-168159163-T-C
• rs1517342
• NM_013233.3:c.628+2624A>G

Variant summary

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

The NM_013233.3(STK39):​c.628+2624A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,010 control chromosomes in the GnomAD database, including 18,981 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 0.50 (18981 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013233.3. 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
	STK39	NM_013233.3	MANE Select	c.628+2624A>G		intron	N/A	NP_037365.2	Q9UEW8-1
	STK39	NM_001410961.1		c.628+2624A>G		intron	N/A	NP_001397890.1	A0A8V8TKT5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK39	ENST00000355999.5	TSL:1 MANE Select	c.628+2624A>G		intron	N/A	ENSP00000348278.4	Q9UEW8-1
	STK39	ENST00000952313.1		c.628+2624A>G		intron	N/A	ENSP00000622372.1
	STK39	ENST00000697205.1		c.628+2624A>G		intron	N/A	ENSP00000513185.1	A0A8V8TKT5

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75506 AN: 151892 Hom.: 18967 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.497 AC: 75565 AN: 152010 Hom.: 18981 Cov.: 32 AF XY: 0.496 AC XY: 36856 AN XY: 74302

African (AFR) AF: 0.474 AC: 19659 AN: 41432

American (AMR) AF: 0.456 AC: 6970 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3264 AN: 5176

South Asian (SAS) AF: 0.452 AC: 2173 AN: 4808

European-Finnish (FIN) AF: 0.546 AC: 5772 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34662 AN: 67966

Other (OTH) AF: 0.486 AC: 1026 AN: 2110

Alfa AF: 0.501 Hom.: 26513

Bravo AF: 0.491

Asia WGS AF: 0.497 AC: 1725 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.65
PhyloP100		-2.4
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: rs1517342; hg19: chr2-169015673;