rs13419175

Positions:

• chr2-168131429-A-C
• chr2-168131429-A-G
• chr2-168131429-A-T

Variant summary

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

The NM_013233.3(STK39):​c.975-1671T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,046 control chromosomes in the GnomAD database, including 49,614 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 0.81 (49614 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK39	NM_013233.3	c.975-1671T>G		intron_variant		ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.975-1671T>G		intron_variant		1	NM_013233.3	ENSP00000348278	P1
STK39	ENST00000697205.1	c.975-1671T>G		intron_variant				ENSP00000513185

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122792 AN: 151928 Hom.: 49582 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.808 AC: 122879 AN: 152046 Hom.: 49614 Cov.: 31 AF XY: 0.812 AC XY: 60313 AN XY: 74322

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.778

Alfa AF: 0.814 Hom.: 17694

Bravo AF: 0.806

Asia WGS AF: 0.790 AC: 2747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.74

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: rs13419175; hg19: chr2-168987939;