rs1517343

Positions:

• chr2-168159465-C-A
• chr2-168159465-C-G
• chr2-168159465-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_013233.3(STK39):​c.628+2322G>T 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 151,916 control chromosomes in the GnomAD database, including 18,964 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 (18964 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK39	NM_013233.3	c.628+2322G>T		intron_variant		ENST00000355999.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK39	ENST00000355999.5	c.628+2322G>T		intron_variant		1	NM_013233.3	P1
STK39	ENST00000697205.1	c.628+2322G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75470 AN: 151796 Hom.: 18950 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.487

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: 75529 AN: 151916 Hom.: 18964 Cov.: 31 AF XY: 0.496 AC XY: 36845 AN XY: 74274

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.486

Alfa AF: 0.500 Hom.: 8702

Bravo AF: 0.491

Asia WGS AF: 0.497 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	21
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.43		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.43		Position offset: -5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1517343; hg19: chr2-169015975;