chr2-168182743-G-C

Variant names:

• chr2-168182743-G-C
• rs12692877
• NM_013233.3:c.209-653C>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_013233.3(STK39):​c.209-653C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,062 control chromosomes in the GnomAD database, including 7,940 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 0.32 (7940 hom., cov: 33)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.209-653C>G		intron_variant	Intron 1 of 17	ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.209-653C>G		intron_variant	Intron 1 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.209-653C>G		intron_variant	Intron 1 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48352 AN: 151944 Hom.: 7933 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.318 AC: 48382 AN: 152062 Hom.: 7940 Cov.: 33 AF XY: 0.323 AC XY: 24019 AN XY: 74356

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.333

Alfa AF: 0.161 Hom.: 295

Bravo AF: 0.327

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.50

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: rs12692877; hg19: chr2-169039253;