9-77794896-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002072.5(GNAQ):c.606-304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,958 control chromosomes in the GnomAD database, including 25,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (25015 hom., cov: 32)
• Consequence: GNAQ NM_002072.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.303

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 9-77794896-G-A is Benign according to our data. Variant chr9-77794896-G-A is described in ClinVar as [Benign]. Clinvar id is 1279961.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNAQ	NM_002072.5	c.606-304C>T		intron_variant		ENST00000286548.9
GNAQ	XM_047423239.1	c.432-304C>T		intron_variant
GNAQ	XM_047423240.1	c.432-304C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAQ	ENST00000286548.9	c.606-304C>T		intron_variant		1	NM_002072.5	P1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82194 AN: 151840 Hom.: 25015 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82211 AN: 151958 Hom.: 25015 Cov.: 32 AF XY: 0.540 AC XY: 40123 AN XY: 74242

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.574

Alfa AF: 0.586 Hom.: 3486

Bravo AF: 0.522

Asia WGS AF: 0.558 AC: 1939 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.46

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

Other links and lift over

dbSNP: rs4361824; hg19: chr9-80409812;