9-77720160-C-T

Position:

• chr9-77720160-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002072.5(GNAQ):​c.*1163G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 232,876 control chromosomes in the GnomAD database, including 42,939 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.55 (25959 hom., cov: 32)
  • Exomes 𝑓: 0.64 (16980 hom.)
• Consequence: GNAQ NM_002072.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNAQ	NM_002072.5	c.*1163G>A		3_prime_UTR_variant	7/7	ENST00000286548.9
GNAQ	XM_047423239.1	c.*1163G>A		3_prime_UTR_variant	7/7
GNAQ	XM_047423240.1	c.*1163G>A		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNAQ	ENST00000286548.9	c.*1163G>A		3_prime_UTR_variant	7/7	1	NM_002072.5	P1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83416 AN: 151926 Hom.: 25966 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.586

GnomAD4 exome AF: 0.638 AC: 51606 AN: 80832 Hom.: 16980 Cov.: 0 AF XY: 0.641 AC XY: 23839 AN XY: 37168

Gnomad4 AFR exome AF: 0.232

Gnomad4 AMR exome AF: 0.599

Gnomad4 ASJ exome AF: 0.657

Gnomad4 EAS exome AF: 0.539

Gnomad4 SAS exome AF: 0.650

Gnomad4 FIN exome AF: 0.685

Gnomad4 NFE exome AF: 0.695

Gnomad4 OTH exome AF: 0.617

GnomAD4 genome AF: 0.549 AC: 83427 AN: 152044 Hom.: 25959 Cov.: 32 AF XY: 0.549 AC XY: 40777 AN XY: 74326

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.586

Alfa AF: 0.560 Hom.: 3842

Bravo AF: 0.526

Asia WGS AF: 0.548 AC: 1910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.75

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: rs3858119; hg19: chr9-80335076;