chr20-44972032-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006282.5(STK4):c.36-46C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,547,962 control chromosomes in the GnomAD database, including 175,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.50 ( 20040 hom., cov: 32)
Exomes 𝑓: 0.47 ( 155764 hom. )
Consequence
STK4
NM_006282.5 intron
NM_006282.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.304
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 20-44972032-C-G is Benign according to our data. Variant chr20-44972032-C-G is described in ClinVar as [Benign]. Clinvar id is 1334913.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK4 | NM_006282.5 | c.36-46C>G | intron_variant | ENST00000372806.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK4 | ENST00000372806.8 | c.36-46C>G | intron_variant | 1 | NM_006282.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.503 AC: 76441AN: 151852Hom.: 20003 Cov.: 32
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GnomAD3 exomes AF: 0.443 AC: 109470AN: 247332Hom.: 26051 AF XY: 0.447 AC XY: 59937AN XY: 134108
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GnomAD4 exome AF: 0.466 AC: 650967AN: 1395992Hom.: 155764 Cov.: 21 AF XY: 0.465 AC XY: 325057AN XY: 698330
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GnomAD4 genome ? AF: 0.504 AC: 76529AN: 151970Hom.: 20040 Cov.: 32 AF XY: 0.502 AC XY: 37272AN XY: 74264
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | 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: 54. Only high quality variants are reported. - |
Combined immunodeficiency due to STK4 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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