chr12-27297738-G-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_015000.4(STK38L):c.18G>T(p.Gly6=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00474 in 1,613,786 control chromosomes in the GnomAD database, including 304 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.025 ( 158 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 146 hom. )
Consequence
STK38L
NM_015000.4 synonymous
NM_015000.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.27
Genes affected
STK38L (HGNC:17848): (serine/threonine kinase 38 like) Enables ATP binding activity; magnesium ion binding activity; and protein serine/threonine kinase activity. Involved in intracellular signal transduction. Acts upstream of or within protein phosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 12-27297738-G-T is Benign according to our data. Variant chr12-27297738-G-T is described in ClinVar as [Benign]. Clinvar id is 786605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK38L | NM_015000.4 | c.18G>T | p.Gly6= | synonymous_variant | 2/14 | ENST00000389032.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK38L | ENST00000389032.8 | c.18G>T | p.Gly6= | synonymous_variant | 2/14 | 1 | NM_015000.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0254 AC: 3858AN: 152120Hom.: 158 Cov.: 32
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GnomAD3 exomes AF: 0.00671 AC: 1687AN: 251308Hom.: 75 AF XY: 0.00459 AC XY: 624AN XY: 135838
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GnomAD4 exome AF: 0.00260 AC: 3794AN: 1461548Hom.: 146 Cov.: 30 AF XY: 0.00220 AC XY: 1601AN XY: 727064
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GnomAD4 genome ? AF: 0.0254 AC: 3860AN: 152238Hom.: 158 Cov.: 32 AF XY: 0.0237 AC XY: 1761AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2017 | - - |
STK38L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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