rs1517343

Variant names:

• chr2-168159465-C-A
• rs1517343
• NM_013233.3:c.628+2322G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-168159465-C-A
• chr2-168159465-C-G
• chr2-168159465-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_013233.3(STK39):​c.628+2322G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,916 control chromosomes in the GnomAD database, including 18,964 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 0.50 (18964 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.628+2322G>T		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+2322G>T		intron_variant	Intron 5 of 17	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.628+2322G>T		intron_variant	Intron 5 of 16			ENSP00000513185.1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75470 AN: 151796 Hom.: 18950 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.497 AC: 75529 AN: 151916 Hom.: 18964 Cov.: 31 AF XY: 0.496 AC XY: 36845 AN XY: 74274

African (AFR) AF: 0.475 AC: 19664 AN: 41406

American (AMR) AF: 0.456 AC: 6968 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3472

East Asian (EAS) AF: 0.631 AC: 3258 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2165 AN: 4792

European-Finnish (FIN) AF: 0.547 AC: 5771 AN: 10554

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34641 AN: 67942

Other (OTH) AF: 0.486 AC: 1023 AN: 2104

Alfa AF: 0.501 Hom.: 9820

Bravo AF: 0.491

Asia WGS AF: 0.497 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	21
DANN	Benign	0.80
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.43		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.43		Position offset: -5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1517343; hg19: chr2-169015975;