rs559674838
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 1P and 18B. PP2BP4_ModerateBP6_Very_StrongBS1BS2
The NM_020988.3(GNAO1):c.286G>A(p.Gly96Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,613,824 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G96A) has been classified as Uncertain significance.
Frequency
Consequence
NM_020988.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.286G>A | p.Gly96Ser | missense_variant | 3/9 | ENST00000262493.12 | |
GNAO1 | NM_138736.3 | c.286G>A | p.Gly96Ser | missense_variant | 3/8 | ||
GNAO1 | XM_011523003.4 | c.160G>A | p.Gly54Ser | missense_variant | 3/9 | ||
GNAO1 | XR_007064866.1 | n.1033G>A | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAO1 | ENST00000262493.12 | c.286G>A | p.Gly96Ser | missense_variant | 3/9 | 1 | NM_020988.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251052Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135674
GnomAD4 exome AF: 0.000105 AC: 153AN: 1461518Hom.: 0 Cov.: 30 AF XY: 0.000103 AC XY: 75AN XY: 727066
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74488
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2018 | 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. - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 12, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 16, 2021 | - - |
Intellectual disability Benign:1
Likely benign, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at