rs1517320

Positions:

• chr2-168225732-A-G
• chr2-168225732-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.208+21496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,112 control chromosomes in the GnomAD database, including 49,241 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 0.80 (49241 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK39	NM_013233.3	c.208+21496T>C		intron_variant		ENST00000355999.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK39	ENST00000355999.5	c.208+21496T>C		intron_variant		1	NM_013233.3	P1
STK39	ENST00000697205.1	c.208+21496T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122295 AN: 151994 Hom.: 49203 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.805 AC: 122386 AN: 152112 Hom.: 49241 Cov.: 31 AF XY: 0.806 AC XY: 59945 AN XY: 74362

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.798

Alfa AF: 0.819 Hom.: 103312

Bravo AF: 0.800

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.64

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: rs1517320; hg19: chr2-169082242;