5-123614379-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001364140.2(CSNK1G3):āc.1354A>Gā(p.Ile452Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001364140.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSNK1G3 | NM_001364140.2 | c.1354A>G | p.Ile452Val | missense_variant | 14/14 | ENST00000696905.1 | NP_001351069.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSNK1G3 | ENST00000696905.1 | c.1354A>G | p.Ile452Val | missense_variant | 14/14 | NM_001364140.2 | ENSP00000512966.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250408Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135342
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1461036Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726814
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2024 | The c.1351A>G (p.I451V) alteration is located in exon 14 (coding exon 13) of the CSNK1G3 gene. This alteration results from a A to G substitution at nucleotide position 1351, causing the isoleucine (I) at amino acid position 451 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at