16-56192244-T-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020988.3(GNAO1):c.9T>C(p.Cys3Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000021 in 1,431,602 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 (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
GNAO1
NM_020988.3 synonymous
NM_020988.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.30
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 16-56192244-T-C is Benign according to our data. Variant chr16-56192244-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2988258.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.3 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GNAO1 | NM_020988.3 | c.9T>C | p.Cys3Cys | synonymous_variant | Exon 1 of 9 | ENST00000262493.12 | NP_066268.1 | |
| GNAO1 | NM_138736.3 | c.9T>C | p.Cys3Cys | synonymous_variant | Exon 1 of 8 | NP_620073.2 | ||
| GNAO1 | XR_007064866.1 | n.756T>C | non_coding_transcript_exon_variant | Exon 1 of 9 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1431602Hom.: 0 Cov.: 28 AF XY: 0.00000421 AC XY: 3AN XY: 712328 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1431602
Hom.:
Cov.:
28
AF XY:
AC XY:
3
AN XY:
712328
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32856
American (AMR)
AF:
AC:
0
AN:
43400
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25720
East Asian (EAS)
AF:
AC:
0
AN:
39018
South Asian (SAS)
AF:
AC:
0
AN:
83890
European-Finnish (FIN)
AF:
AC:
0
AN:
51188
Middle Eastern (MID)
AF:
AC:
0
AN:
5732
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1090466
Other (OTH)
AF:
AC:
0
AN:
59332
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Developmental and epileptic encephalopathy Benign:1
Feb 27, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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