NM_013233.3:c.321+897G>A

Variant names:

• chr2-168181081-C-T
• rs10930309
• NM_013233.3:c.321+897G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_013233.3(STK39):​c.321+897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,136 control chromosomes in the GnomAD database, including 4,727 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 0.22 (4727 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.321+897G>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+897G>A		intron_variant	Intron 2 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.321+897G>A		intron_variant	Intron 2 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33718 AN: 152018 Hom.: 4728 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.222 AC: 33709 AN: 152136 Hom.: 4727 Cov.: 32 AF XY: 0.218 AC XY: 16202 AN XY: 74360

African (AFR) AF: 0.0726 AC: 3016 AN: 41540

American (AMR) AF: 0.165 AC: 2526 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3468

East Asian (EAS) AF: 0.0705 AC: 366 AN: 5188

South Asian (SAS) AF: 0.174 AC: 838 AN: 4818

European-Finnish (FIN) AF: 0.302 AC: 3184 AN: 10550

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22307 AN: 67978

Other (OTH) AF: 0.213 AC: 451 AN: 2116

Alfa AF: 0.256 Hom.: 1694

Bravo AF: 0.204

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.66
PhyloP100		0.89
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: rs10930309; hg19: chr2-169037591;