chr20-44975362-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006282.5(STK4):c.117-3081C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 980,010 control chromosomes in the GnomAD database, including 117,487 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 22329 hom., cov: 32)
Exomes 𝑓: 0.48 ( 95158 hom. )
Consequence
STK4
NM_006282.5 intron
NM_006282.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.751
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 20-44975362-C-T is Benign according to our data. Variant chr20-44975362-C-T is described in ClinVar as [Benign]. Clinvar id is 2688087.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK4 | NM_006282.5 | c.117-3081C>T | intron_variant | ENST00000372806.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK4 | ENST00000372806.8 | c.117-3081C>T | intron_variant | 1 | NM_006282.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.529 AC: 80332AN: 151906Hom.: 22287 Cov.: 32
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GnomAD4 exome AF: 0.477 AC: 394578AN: 827984Hom.: 95158 Cov.: 29 AF XY: 0.476 AC XY: 182243AN XY: 382520
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 56% of patients studied by a panel of primary immunodeficiencies. Number of patients: 53. Only high quality variants are reported. - |
Computational scores
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Cadd
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at