9-77728669-T-TG

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

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 5.49
Variant links:
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]

Genome browser will be placed here

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
GNAQNM_002072.5 linkuse as main transcriptc.736-3_736-2insC splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000286548.9 NP_002063.2
GNAQXM_047423239.1 linkuse as main transcriptc.562-3_562-2insC splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant XP_047279195.1
GNAQXM_047423240.1 linkuse as main transcriptc.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
GNAQENST00000286548.9 linkuse as main transcriptc.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:
12
AN:
86358
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000356
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000288
Gnomad OTH
AF:
0.000887
GnomAD3 exomes
AF:
0.0000666
AC:
12
AN:
180240
Hom.:
0
AF XY:
0.0000605
AC XY:
6
AN XY:
99174
show subpopulations
Gnomad AFR exome
AF:
0.000143
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000111
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000167
AC:
229
AN:
1371404
Hom.:
0
Cov.:
26
AF XY:
0.000164
AC XY:
112
AN XY:
683076
show subpopulations
Gnomad4 AFR exome
AF:
0.000201
Gnomad4 AMR exome
AF:
0.0000306
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000257
Gnomad4 SAS exome
AF:
0.0000514
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000187
Gnomad4 OTH exome
AF:
0.000335
GnomAD4 genome
AF:
0.000139
AC:
12
AN:
86462
Hom.:
0
Cov.:
30
AF XY:
0.000189
AC XY:
8
AN XY:
42370
show subpopulations
Gnomad4 AFR
AF:
0.0000355
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000288
Gnomad4 OTH
AF:
0.000876

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 providedclinical testingPreventionGenetics, part of Exact SciencesApr 05, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs757232284; hg19: chr9-80343585; API