chr2-168225732-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013233.3(STK39):​c.208+21496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,112 control chromosomes in the GnomAD database, including 49,241 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 0.80 ( 49241 hom., cov: 31)

Consequence

STK39
NM_013233.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STK39NM_013233.3 linkuse as main transcriptc.208+21496T>C intron_variant ENST00000355999.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK39ENST00000355999.5 linkuse as main transcriptc.208+21496T>C intron_variant 1 NM_013233.3 P1Q9UEW8-1
STK39ENST00000697205.1 linkuse as main transcriptc.208+21496T>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.805
AC:
122295
AN:
151994
Hom.:
49203
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.792
Gnomad AMI
AF:
0.792
Gnomad AMR
AF:
0.766
Gnomad ASJ
AF:
0.843
Gnomad EAS
AF:
0.746
Gnomad SAS
AF:
0.766
Gnomad FIN
AF:
0.826
Gnomad MID
AF:
0.788
Gnomad NFE
AF:
0.823
Gnomad OTH
AF:
0.799
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.805
AC:
122386
AN:
152112
Hom.:
49241
Cov.:
31
AF XY:
0.806
AC XY:
59945
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.792
Gnomad4 AMR
AF:
0.766
Gnomad4 ASJ
AF:
0.843
Gnomad4 EAS
AF:
0.745
Gnomad4 SAS
AF:
0.767
Gnomad4 FIN
AF:
0.826
Gnomad4 NFE
AF:
0.823
Gnomad4 OTH
AF:
0.798
Alfa
AF:
0.819
Hom.:
103312
Bravo
AF:
0.800
Asia WGS
AF:
0.778
AC:
2707
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.9
DANN
Benign
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1517320; hg19: chr2-169082242; API