ENST00000487143.5:n.1787T>A

Variant names:

• chr2-167954447-A-T
• rs7425806
• ENST00000487143.5:n.1787T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000487143.5(STK39):​n.1787T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: STK39 ENST00000487143.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK39	NM_013233.3	c.*1049T>A		3_prime_UTR_variant	Exon 18 of 18	ENST00000355999.5	NP_037365.2
STK39	NM_001410961.1	c.*1049T>A		3_prime_UTR_variant	Exon 17 of 17		NP_001397890.1
STK39	XM_047443944.1	c.*1049T>A		3_prime_UTR_variant	Exon 18 of 18		XP_047299900.1
STK39	XM_017003817.3	c.*1049T>A		3_prime_UTR_variant	Exon 15 of 15		XP_016859306.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000487143.5	n.1787T>A		non_coding_transcript_exon_variant	Exon 9 of 9	1
STK39	ENST00000355999.5	c.*1049T>A		3_prime_UTR_variant	Exon 18 of 18	1	NM_013233.3	ENSP00000348278.4
STK39	ENST00000697205.1	c.*1049T>A		3_prime_UTR_variant	Exon 17 of 17			ENSP00000513185.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.97

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: rs7425806; hg19: chr2-168810957;