Variant 9-77728671-GAAA-GAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_002072.5(GNAQ):c.736-5delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 1,295,286 control chromosomes in the GnomAD database, including 110 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 102 hom., cov: 0)

Exomes 𝑓: 0.031 ( 8 hom. )

Consequence

GNAQ
NM_002072.5 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.572

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 Benign. Variant got -16 ACMG points.

BP6

Variant 9-77728671-GA-G is Benign according to our data. Variant chr9-77728671-GA-G is described in ClinVar as [Benign]. Clinvar id is 776427.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-77728671-GA-G is described in Lovd as [Benign]. Variant chr9-77728671-GA-G is described in Lovd as [Benign]. Variant chr9-77728671-GA-G is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GNAQ	NM_002072.5 link	c.736-5delT	splice_region_variant, intron_variant	Intron 5 of 6	ENST00000286548.9	NP_002063.2	P50148A0A024R240
GNAQ	XM_047423239.1 link	c.562-5delT	splice_region_variant, intron_variant	Intron 5 of 6		XP_047279195.1
GNAQ	XM_047423240.1 link	c.562-5delT	splice_region_variant, intron_variant	Intron 5 of 6		XP_047279196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAQ	ENST00000286548.9 link	c.736-5delT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_002072.5	ENSP00000286548.4		P50148

Frequencies

GnomAD3 genomes

AF:

0.0183

AC:

2659

AN:

145548

Hom.:

102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0621

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00770

Gnomad ASJ

AF:

0.000292

Gnomad EAS

AF:

0.00304

Gnomad SAS

AF:

0.000647

Gnomad FIN

AF:

0.00138

Gnomad MID

AF:

0.00662

Gnomad NFE

AF:

0.000511

Gnomad OTH

AF:

0.0131

GnomAD4 exome

AF:

0.0307

AC:

35312

AN:

1149670

Hom.:

Cov.:

AF XY:

0.0311

AC XY:

17934

AN XY:

576428

show subpopulations

Gnomad4 AFR exome

AF:

0.111

Gnomad4 AMR exome

AF:

0.0396

Gnomad4 ASJ exome

AF:

0.0346

Gnomad4 EAS exome

AF:

0.0668

Gnomad4 SAS exome

AF:

0.0436

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.0251

Gnomad4 OTH exome

AF:

0.0360

GnomAD4 genome

AF:

0.0184

AC:

2673

AN:

145616

Hom.:

102

Cov.:

AF XY:

0.0176

AC XY:

1240

AN XY:

70570

show subpopulations

Gnomad4 AFR

AF:

0.0623

Gnomad4 AMR

AF:

0.00769

Gnomad4 ASJ

AF:

0.000292

Gnomad4 EAS

AF:

0.00304

Gnomad4 SAS

AF:

0.000650

Gnomad4 FIN

AF:

0.00138

Gnomad4 NFE

AF:

0.000512

Gnomad4 OTH

AF:

0.0129

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

Jun 30, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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