rs3754775

chr2-168159753-C-T

Variant summary

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

The NM_013233.3(STK39):c.628+2034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,110 control chromosomes in the GnomAD database, including 2,298 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 0.16 (2298 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK39	NM_013233.3	c.628+2034G>A		intron_variant		ENST00000355999.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK39	ENST00000355999.5	c.628+2034G>A		intron_variant		1	NM_013233.3	P1
STK39	ENST00000697205.1	c.628+2034G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23956 AN: 151992 Hom.: 2290 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.158 AC: 23980 AN: 152110 Hom.: 2298 Cov.: 32 AF XY: 0.162 AC XY: 12079 AN XY: 74348

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.161

Alfa AF: 0.110 Hom.: 794

Bravo AF: 0.164

Asia WGS AF: 0.229 AC: 794 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	6.8
Dann	Benign	0.59

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: rs3754775; hg19: chr2-169016263;