Variant 9-77728669-T-TG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

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 (★).

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 criteria provided, single submitter 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]

GNAQ links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 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 criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
GNAQ	NM_002072.5 linkuse as main transcript	c.736-3_736-2insC	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	ENST00000286548.9
GNAQ	XM_047423239.1 linkuse as main transcript	c.562-3_562-2insC	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant
GNAQ	XM_047423240.1 linkuse as main transcript	c.562-3_562-2insC	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAQ	ENST00000286548.9 linkuse as main transcript	c.736-3_736-2insC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_002072.5	P1

Frequencies

GnomAD3 genomes

AF:

0.000139

AC:

AN:

86358

Hom.:

Cov.:

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:

AN:

180240

Hom.:

AF XY:

0.0000605

AC XY:

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.:

Cov.:

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:

AN:

86462

Hom.:

Cov.:

AF XY:

0.000189

AC XY:

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: criteria provided, single submitter

LINK: link

Submissions by phenotype

GNAQ-related disorder

Benign:1

Likely benign, criteria provided, single submitter

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over