2-168179226-A-G

Variant names:

• chr2-168179226-A-G
• rs35929607
• NM_013233.3:c.321+2752T>C

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+2752T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,054 control chromosomes in the GnomAD database, including 6,359 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 0.27 (6359 hom., cov: 32)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 20 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=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.321+2752T>C		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+2752T>C		intron_variant	Intron 2 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.321+2752T>C		intron_variant	Intron 2 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41115 AN: 151936 Hom.: 6352 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.271 AC: 41164 AN: 152054 Hom.: 6359 Cov.: 32 AF XY: 0.273 AC XY: 20277 AN XY: 74318

African (AFR) AF: 0.378 AC: 15689 AN: 41460

American (AMR) AF: 0.287 AC: 4381 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3470

East Asian (EAS) AF: 0.560 AC: 2881 AN: 5142

South Asian (SAS) AF: 0.286 AC: 1378 AN: 4816

European-Finnish (FIN) AF: 0.247 AC: 2614 AN: 10576

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12601 AN: 67988

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.229 Hom.: 577

Bravo AF: 0.281

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs35929607; hg19: chr2-169035736;