16-56192289-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_020988.3(GNAO1):c.54G>A(p.Ala18Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020988.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.54G>A | p.Ala18Ala | synonymous_variant | Exon 1 of 9 | ENST00000262493.12 | NP_066268.1 | |
GNAO1 | NM_138736.3 | c.54G>A | p.Ala18Ala | synonymous_variant | Exon 1 of 8 | NP_620073.2 | ||
GNAO1 | XR_007064866.1 | n.801G>A | non_coding_transcript_exon_variant | Exon 1 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247042Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134444
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1459676Hom.: 0 Cov.: 29 AF XY: 0.0000358 AC XY: 26AN XY: 726146
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at