rs11892008

Variant names:

• chr2-168179163-C-T
• rs11892008
• NM_013233.3:c.321+2815G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013233.3(STK39):​c.321+2815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,072 control chromosomes in the GnomAD database, including 2,533 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 (2533 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.321+2815G>A		intron_variant	Intron 2 of 17	ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.321+2815G>A		intron_variant	Intron 2 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.321+2815G>A		intron_variant	Intron 2 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24833 AN: 151954 Hom.: 2524 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24866 AN: 152072 Hom.: 2533 Cov.: 32 AF XY: 0.168 AC XY: 12500 AN XY: 74340

African (AFR) AF: 0.275 AC: 11408 AN: 41460

American (AMR) AF: 0.170 AC: 2595 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5164

South Asian (SAS) AF: 0.162 AC: 779 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1600 AN: 10556

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6628 AN: 67998

Other (OTH) AF: 0.165 AC: 348 AN: 2110

Alfa AF: 0.134 Hom.: 200

Bravo AF: 0.170

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.95
DANN	Benign	0.72
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11892008; hg19: chr2-169035673;