rs2492651
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173575.4(STK32C):c.262+3076G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,154 control chromosomes in the GnomAD database, including 53,460 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 0.83 ( 53460 hom., cov: 31)
Consequence
STK32C
NM_173575.4 intron
NM_173575.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.380
Genes affected
STK32C (HGNC:21332): (serine/threonine kinase 32C) The protein encoded by this gene is a member of the serine/threonine protein kinase family. It is thought that this family member is functional in brain due to its high expression levels there. DNA methylation differences have been found in this gene in monozygotic twins that are discordant for adolescent depression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK32C | NM_173575.4 | c.262+3076G>A | intron_variant | ENST00000298630.8 | NP_775846.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK32C | ENST00000298630.8 | c.262+3076G>A | intron_variant | 1 | NM_173575.4 | ENSP00000298630.3 | ||||
STK32C | ENST00000368622.5 | c.-90+2426G>A | intron_variant | 1 | ENSP00000357611.1 | |||||
STK32C | ENST00000368620.2 | c.301+26940G>A | intron_variant | 3 | ENSP00000357609.3 |
Frequencies
GnomAD3 genomes AF: 0.832 AC: 126561AN: 152036Hom.: 53393 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.833 AC: 126690AN: 152154Hom.: 53460 Cov.: 31 AF XY: 0.833 AC XY: 61987AN XY: 74386
GnomAD4 genome
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31
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2931
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
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