2-168131429-A-C

Variant names:

• chr2-168131429-A-C
• rs13419175
• NM_013233.3:c.975-1671T>G

Variant summary

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

The NM_013233.3(STK39):​c.975-1671T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,046 control chromosomes in the GnomAD database, including 49,614 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 0.81 (49614 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.975-1671T>G		intron_variant	Intron 8 of 17	ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.975-1671T>G		intron_variant	Intron 8 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.975-1671T>G		intron_variant	Intron 8 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122792 AN: 151928 Hom.: 49582 Cov.: 31

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.808 AC: 122879 AN: 152046 Hom.: 49614 Cov.: 31 AF XY: 0.812 AC XY: 60313 AN XY: 74322

African (AFR) AF: 0.810 AC: 33560 AN: 41438

American (AMR) AF: 0.822 AC: 12574 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2896 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4051 AN: 5166

South Asian (SAS) AF: 0.799 AC: 3842 AN: 4806

European-Finnish (FIN) AF: 0.844 AC: 8931 AN: 10586

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54433 AN: 67976

Other (OTH) AF: 0.778 AC: 1642 AN: 2110

Alfa AF: 0.809 Hom.: 21559

Bravo AF: 0.806

Asia WGS AF: 0.790 AC: 2747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.45
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: rs13419175; hg19: chr2-168987939;