chr2-168007850-T-C

Position:

• chr2-168007850-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013233.3(STK39):​c.1498+4784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,966 control chromosomes in the GnomAD database, including 19,104 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 0.49 (19104 hom., cov: 31)
• Consequence: STK39 NM_013233.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK39	NM_013233.3	c.1498+4784A>G		intron_variant		ENST00000355999.5	NP_037365.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK39	ENST00000355999.5	c.1498+4784A>G		intron_variant		1	NM_013233.3	ENSP00000348278	P1
STK39	ENST00000487143.5	n.598+4784A>G		intron_variant, non_coding_transcript_variant		1
STK39	ENST00000697205.1	c.1435+4784A>G		intron_variant				ENSP00000513185
STK39	ENST00000461000.1	n.28+4784A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73760 AN: 151848 Hom.: 19095 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.486 AC: 73791 AN: 151966 Hom.: 19104 Cov.: 31 AF XY: 0.490 AC XY: 36355 AN XY: 74246

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.477

Alfa AF: 0.531 Hom.: 3498

Bravo AF: 0.470

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs6433027; hg19: chr2-168864360;