chr16-56192350-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_020988.3(GNAO1):c.115C>T(p.Leu39Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L39P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_020988.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.115C>T | p.Leu39Phe | missense_variant | 1/9 | ENST00000262493.12 | |
GNAO1 | NM_138736.3 | c.115C>T | p.Leu39Phe | missense_variant | 1/8 | ||
GNAO1 | XR_007064866.1 | n.862C>T | non_coding_transcript_exon_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAO1 | ENST00000262493.12 | c.115C>T | p.Leu39Phe | missense_variant | 1/9 | 1 | NM_020988.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1413514Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 705822
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
See cases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Oct 10, 2019 | ACMG classification criteria: PM2, PP2, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.