chr9-77794571-T-A
Variant summary
Our verdict is Pathogenic. Variant got 26 ACMG points: 26P and 0B. PS1_Very_StrongPM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_002072.5(GNAQ):c.627A>T(p.Gln209His) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q209L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_002072.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 26 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAQ | NM_002072.5 | c.627A>T | p.Gln209His | missense_variant | 5/7 | ENST00000286548.9 | |
GNAQ | XM_047423239.1 | c.453A>T | p.Gln151His | missense_variant | 5/7 | ||
GNAQ | XM_047423240.1 | c.453A>T | p.Gln151His | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAQ | ENST00000286548.9 | c.627A>T | p.Gln209His | missense_variant | 5/7 | 1 | NM_002072.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 27
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Familial multiple nevi flammei Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | - | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital | Jan 31, 2022 | This variant has previously been reported as a somatic change in patients with vascular anomalies (PMID: 27058448, PMID: 30677207, PMID: 29574926) and is absent from large population databases (Genome Aggregation Database v2.1.1). Somatic mutations altering amino acid residue p.Gln209 have been described in multiple vascular anomalies (PMID: 27058448, PMID: 30677207, PMID: 29574926) Alteration of p.Gln209 in GNAQ is a recurrent oncogenic hotspot reported in the cBioPortal and NCI Genomic Data Commons cancer databases, with p.Gln209His reported in multiple melanoma samples (PMID: 24882516). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.