Variant 9-77794429-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002072.5(GNAQ):c.735+34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 1,438,706 control chromosomes in the GnomAD database, including 207,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 16258 hom., cov: 31)

Exomes 𝑓: 0.53 ( 190778 hom. )

Consequence

GNAQ
NM_002072.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.605

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 9-77794429-A-G is Benign according to our data. Variant chr9-77794429-A-G is described in ClinVar as [Benign]. Clinvar id is 1234387.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
GNAQ	NM_002072.5 linkuse as main transcript	c.735+34T>C	intron_variant	ENST00000286548.9	NP_002063.2
GNAQ	XM_047423239.1 linkuse as main transcript	c.561+34T>C	intron_variant		XP_047279195.1
GNAQ	XM_047423240.1 linkuse as main transcript	c.561+34T>C	intron_variant		XP_047279196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAQ	ENST00000286548.9 linkuse as main transcript	c.735+34T>C		intron_variant		1	NM_002072.5	ENSP00000286548	P1

Frequencies

GnomAD3 genomes

AF:

0.424

AC:

64389

AN:

151826

Hom.:

16260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.475

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.222

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.451

GnomAD3 exomes

AF:

0.481

AC:

105929

AN:

220078

Hom.:

27498

AF XY:

0.492

AC XY:

58664

AN XY:

119286

show subpopulations

Gnomad AFR exome

AF:

0.140

Gnomad AMR exome

AF:

0.454

Gnomad ASJ exome

AF:

0.535

Gnomad EAS exome

AF:

0.232

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.494

Gnomad NFE exome

AF:

0.578

Gnomad OTH exome

AF:

0.498

GnomAD4 exome

AF:

0.534

AC:

686926

AN:

1286762

Hom.:

190778

Cov.:

AF XY:

0.533

AC XY:

343038

AN XY:

643084

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.456

Gnomad4 ASJ exome

AF:

0.526

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.438

Gnomad4 FIN exome

AF:

0.503

Gnomad4 NFE exome

AF:

0.572

Gnomad4 OTH exome

AF:

0.504

GnomAD4 genome

AF:

0.424

AC:

64381

AN:

151944

Hom.:

16258

Cov.:

AF XY:

0.419

AC XY:

31122

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.490

Gnomad4 NFE

AF:

0.573

Gnomad4 OTH

AF:

0.448

Alfa

AF:

0.527

Hom.:

17626

Bravo

AF:

0.409

Asia WGS

AF:

0.307

AC:

1072

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.72

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