rs10497334

Positions:

• chr2-167985026-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.1499-20300G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,226 control chromosomes in the GnomAD database, including 1,212 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 0.11 (1212 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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 (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK39	NM_013233.3	c.1499-20300G>A		intron_variant		ENST00000355999.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK39	ENST00000355999.5	c.1499-20300G>A		intron_variant		1	NM_013233.3	P1
STK39	ENST00000487143.5	n.599-20300G>A		intron_variant, non_coding_transcript_variant		1
STK39	ENST00000697205.1	c.1436-20300G>A		intron_variant
STK39	ENST00000461000.1	n.29-20300G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16088 AN: 152108 Hom.: 1212 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.106 AC: 16082 AN: 152226 Hom.: 1212 Cov.: 32 AF XY: 0.103 AC XY: 7631 AN XY: 74420

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0794

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.138

Alfa AF: 0.121 Hom.: 159

Bravo AF: 0.103

Asia WGS AF: 0.0330 AC: 116 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	6.5
DANN	Benign	0.47

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: rs10497334; hg19: chr2-168841536;