2-168154149-A-G

Variant names:

• chr2-168154149-A-G
• rs2063958
• NM_013233.3:c.628+7638T>C

Variant summary

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

The NM_013233.3(STK39):​c.628+7638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,206 control chromosomes in the GnomAD database, including 1,796 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 0.14 (1796 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.628+7638T>C		intron_variant	Intron 5 of 17	ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.628+7638T>C		intron_variant	Intron 5 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.628+7638T>C		intron_variant	Intron 5 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22025 AN: 152088 Hom.: 1799 Cov.: 32

Gnomad AFR AF: 0.0656

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.145 AC: 22027 AN: 152206 Hom.: 1796 Cov.: 32 AF XY: 0.146 AC XY: 10832 AN XY: 74396

African (AFR) AF: 0.0654 AC: 2717 AN: 41532

American (AMR) AF: 0.220 AC: 3357 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5178

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4816

European-Finnish (FIN) AF: 0.158 AC: 1671 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10959 AN: 68004

Other (OTH) AF: 0.159 AC: 337 AN: 2116

Alfa AF: 0.120 Hom.: 352

Bravo AF: 0.146

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.36
PhyloP100		0.27
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: rs2063958; hg19: chr2-169010659;