rs6073604

Variant summary

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

The NM_006282.5(STK4):​c.1148-1487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,138 control chromosomes in the GnomAD database, including 58,075 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 0.87 ( 58075 hom., cov: 30)

Consequence

STK4
NM_006282.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0720
Variant links:
Genes affected
STK4 (HGNC:11408): (serine/threonine kinase 4) The protein encoded by this gene is a cytoplasmic kinase that is structurally similar to the yeast Ste20p kinase, which acts upstream of the stress-induced mitogen-activated protein kinase cascade. The encoded protein can phosphorylate myelin basic protein and undergoes autophosphorylation. A caspase-cleaved fragment of the encoded protein has been shown to be capable of phosphorylating histone H2B. The particular phosphorylation catalyzed by this protein has been correlated with apoptosis, and it's possible that this protein induces the chromatin condensation observed in this process. [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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STK4NM_006282.5 linkuse as main transcriptc.1148-1487G>A intron_variant ENST00000372806.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK4ENST00000372806.8 linkuse as main transcriptc.1148-1487G>A intron_variant 1 NM_006282.5 P1Q13043-1

Frequencies

GnomAD3 genomes
AF:
0.873
AC:
132653
AN:
152020
Hom.:
58021
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.906
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.865
Gnomad ASJ
AF:
0.799
Gnomad EAS
AF:
0.964
Gnomad SAS
AF:
0.889
Gnomad FIN
AF:
0.914
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.844
Gnomad OTH
AF:
0.864
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.873
AC:
132767
AN:
152138
Hom.:
58075
Cov.:
30
AF XY:
0.876
AC XY:
65201
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.906
Gnomad4 AMR
AF:
0.865
Gnomad4 ASJ
AF:
0.799
Gnomad4 EAS
AF:
0.964
Gnomad4 SAS
AF:
0.888
Gnomad4 FIN
AF:
0.914
Gnomad4 NFE
AF:
0.844
Gnomad4 OTH
AF:
0.866
Alfa
AF:
0.846
Hom.:
58973
Bravo
AF:
0.872
Asia WGS
AF:
0.926
AC:
3221
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
6.5
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs6073604; hg19: chr20-43652127; API