rs201331473
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_173354.5(SIK1):c.306C>T(p.Val102Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_173354.5 synonymous
Scores
Clinical Significance
Conservation
Publications
- developmental and epileptic encephalopathy, 30Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- early myoclonic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- infantile spasmsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- generalized epilepsyInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIK1 | ENST00000270162.8 | c.306C>T | p.Val102Val | synonymous_variant | Exon 4 of 14 | 1 | NM_173354.5 | ENSP00000270162.6 | ||
SIK1 | ENST00000644750.1 | c.306C>T | p.Val102Val | synonymous_variant | Exon 4 of 5 | ENSP00000495479.1 | ||||
SIK1 | ENST00000478426.1 | n.1C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
SIK1 | ENST00000644689.1 | n.108C>T | non_coding_transcript_exon_variant | Exon 1 of 5 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD2 exomes AF: 0.000207 AC: 52AN: 251358 AF XY: 0.000199 show subpopulations
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 0
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Developmental and epileptic encephalopathy, 30 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at