rs6714609

Variant names:

• chr2-168153740-G-A
• rs6714609
• NM_013233.3:c.628+8047C>T

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+8047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,832 control chromosomes in the GnomAD database, including 14,350 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 0.41 (14350 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013233.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK39	NM_013233.3	MANE Select	c.628+8047C>T		intron	N/A	NP_037365.2	Q9UEW8-1
	STK39	NM_001410961.1		c.628+8047C>T		intron	N/A	NP_001397890.1	A0A8V8TKT5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK39	ENST00000355999.5	TSL:1 MANE Select	c.628+8047C>T		intron	N/A	ENSP00000348278.4	Q9UEW8-1
	STK39	ENST00000952313.1		c.628+8047C>T		intron	N/A	ENSP00000622372.1
	STK39	ENST00000697205.1		c.628+8047C>T		intron	N/A	ENSP00000513185.1	A0A8V8TKT5

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61736 AN: 151710 Hom.: 14326 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.407 AC: 61824 AN: 151832 Hom.: 14350 Cov.: 31 AF XY: 0.412 AC XY: 30543 AN XY: 74166

African (AFR) AF: 0.619 AC: 25605 AN: 41370

American (AMR) AF: 0.437 AC: 6677 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3472 AN: 5150

South Asian (SAS) AF: 0.418 AC: 2006 AN: 4796

European-Finnish (FIN) AF: 0.343 AC: 3618 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18359 AN: 67924

Other (OTH) AF: 0.401 AC: 844 AN: 2106

Alfa AF: 0.363 Hom.: 1964

Bravo AF: 0.425

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6714609; hg19: chr2-169010250;