9-77728669-T-TG
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_002072.5(GNAQ):c.736-3_736-2insC variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.000165 in 1,457,866 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
GNAQ
NM_002072.5 splice_region, splice_polypyrimidine_tract, intron
NM_002072.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.49
Genes affected
GNAQ (HGNC:4390): (G protein subunit alpha q) This locus encodes a guanine nucleotide-binding protein. The encoded protein, an alpha subunit in the Gq class, couples a seven-transmembrane domain receptor to activation of phospolipase C-beta. Mutations at this locus have been associated with problems in platelet activation and aggregation. A related pseudogene exists on chromosome 2.[provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP6
Variant 9-77728669-T-TG is Benign according to our data. Variant chr9-77728669-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 3058149.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNAQ | NM_002072.5 | c.736-3_736-2insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000286548.9 | NP_002063.2 | |||
GNAQ | XM_047423239.1 | c.562-3_562-2insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | XP_047279195.1 | ||||
GNAQ | XM_047423240.1 | c.562-3_562-2insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | XP_047279196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNAQ | ENST00000286548.9 | c.736-3_736-2insC | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002072.5 | ENSP00000286548 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000139 AC: 12AN: 86358Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000666 AC: 12AN: 180240Hom.: 0 AF XY: 0.0000605 AC XY: 6AN XY: 99174
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GnomAD4 exome AF: 0.000167 AC: 229AN: 1371404Hom.: 0 Cov.: 26 AF XY: 0.000164 AC XY: 112AN XY: 683076
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GnomAD4 genome AF: 0.000139 AC: 12AN: 86462Hom.: 0 Cov.: 30 AF XY: 0.000189 AC XY: 8AN XY: 42370
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GNAQ-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 05, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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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