rs200402559
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_173354.5(SIK1):c.1538C>T(p.Ala513Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_173354.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 exomes AF: 0.000283 AC: 69AN: 243818Hom.: 0 AF XY: 0.000226 AC XY: 30AN XY: 132616
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000135 AC: 1AN: 7408Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 3852
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 0Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 0
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 30 Uncertain:1Benign:1
SIK1 NM_173354.4 exon 12 p.Ala513Val (c.1538C>T): This variant has not been reported in the literature, but it is present in 0.2% (60/25748) of Finnish alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/21-44838346-G-A). This variant amino acid, valine (Val), is present in one mammal and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant are insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at