rs2241527
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015690.5(STK36):c.-89-240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 343,894 control chromosomes in the GnomAD database, including 18,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 7498 hom., cov: 31)
Exomes 𝑓: 0.33 ( 11403 hom. )
Consequence
STK36
NM_015690.5 intron
NM_015690.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.177
Genes affected
STK36 (HGNC:17209): (serine/threonine kinase 36) This gene encodes a member of the serine/threonine kinase family of enzymes. This family member is similar to a Drosophila protein that plays a key role in the Hedgehog signaling pathway. This human protein is a positive regulator of the GLI zinc-finger transcription factors. Knockout studies of the homologous mouse gene suggest that defects in this human gene may lead to congenital hydrocephalus, possibly due to a functional defect in motile cilia. Because Hedgehog signaling is frequently activated in certain kinds of gastrointestinal cancers, it has been suggested that this gene is a target for the treatment of these cancers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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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=-0.83).
BP6
?
Variant 2-218672501-G-A is Benign according to our data. Variant chr2-218672501-G-A is described in ClinVar as [Benign]. Clinvar id is 1229044.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK36 | NM_015690.5 | c.-89-240G>A | intron_variant | ENST00000295709.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STK36 | ENST00000295709.8 | c.-89-240G>A | intron_variant | 1 | NM_015690.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.280 AC: 42476AN: 151852Hom.: 7498 Cov.: 31
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GnomAD4 exome AF: 0.329 AC: 63071AN: 191924Hom.: 11403 AF XY: 0.322 AC XY: 33457AN XY: 103818
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GnomAD4 genome ? AF: 0.280 AC: 42477AN: 151970Hom.: 7498 Cov.: 31 AF XY: 0.278 AC XY: 20641AN XY: 74248
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at