rs922445
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020988.3(GNAO1):c.304-20484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,142 control chromosomes in the GnomAD database, including 3,011 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3011 hom., cov: 32)
Exomes 𝑓: 0.23 ( 0 hom. )
Consequence
GNAO1
NM_020988.3 intron
NM_020988.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0960
Genes affected
GNAO1 (HGNC:4389): (G protein subunit alpha o1) The protein encoded by this gene represents the alpha subunit of the Go heterotrimeric G-protein signal-transducing complex. Defects in this gene are a cause of early-onset epileptic encephalopathy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.304-20484G>A | intron_variant | ENST00000262493.12 | |||
GNAO1 | NM_138736.3 | c.304-20484G>A | intron_variant | ||||
GNAO1 | XM_011523003.4 | c.178-20484G>A | intron_variant | ||||
GNAO1 | XR_007064866.1 | n.1051-20484G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAO1 | ENST00000262493.12 | c.304-20484G>A | intron_variant | 1 | NM_020988.3 | P1 | |||
ENST00000623118.1 | n.1303G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.191 AC: 29050AN: 151998Hom.: 3008 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.231 AC: 6AN: 26Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4AN XY: 22
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GnomAD4 genome ? AF: 0.191 AC: 29073AN: 152116Hom.: 3011 Cov.: 32 AF XY: 0.194 AC XY: 14421AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at