rs200539902
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_ModerateBP6_ModerateBS1BS2
The NM_020988.3(GNAO1):āc.386T>Cā(p.Met129Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,614,184 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M129I) has been classified as Likely benign.
Frequency
Consequence
NM_020988.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.386T>C | p.Met129Thr | missense_variant | 4/9 | ENST00000262493.12 | |
GNAO1 | NM_138736.3 | c.386T>C | p.Met129Thr | missense_variant | 4/8 | ||
GNAO1 | XM_011523003.4 | c.260T>C | p.Met87Thr | missense_variant | 4/9 | ||
GNAO1 | XR_007064866.1 | n.1133T>C | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAO1 | ENST00000262493.12 | c.386T>C | p.Met129Thr | missense_variant | 4/9 | 1 | NM_020988.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135920
GnomAD4 exome AF: 0.000277 AC: 405AN: 1461862Hom.: 3 Cov.: 31 AF XY: 0.000275 AC XY: 200AN XY: 727238
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74486
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at