9-77720160-C-T

Variant names:

• chr9-77720160-C-T
• rs3858119
• NM_002072.5:c.*1163G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• congenital hemangioma

  Inheritance: AD Classification: STRONG Submitted by: G2P
• Sturge-Weber syndrome

  Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002072.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAQ	NM_002072.5	MANE Select	c.*1163G>A		3_prime_UTR	Exon 7 of 7	NP_002063.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNAQ	ENST00000286548.9	TSL:1 MANE Select	c.*1163G>A		3_prime_UTR	Exon 7 of 7	ENSP00000286548.4	P50148
	GNAQ	ENST00000857199.1		c.*1163G>A		3_prime_UTR	Exon 8 of 8	ENSP00000527258.1
	GNAQ	ENST00000915940.1		c.*1163G>A		3_prime_UTR	Exon 8 of 8	ENSP00000585999.1

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

African (AFR) AF: 0.232 AC: 899 AN: 3882

American (AMR) AF: 0.599 AC: 1490 AN: 2488

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 3352 AN: 5100

East Asian (EAS) AF: 0.539 AC: 6113 AN: 11346

South Asian (SAS) AF: 0.650 AC: 451 AN: 694

European-Finnish (FIN) AF: 0.685 AC: 185 AN: 270

Middle Eastern (MID) AF: 0.657 AC: 323 AN: 492

European-Non Finnish (NFE) AF: 0.695 AC: 34635 AN: 49820

Other (OTH) AF: 0.617 AC: 4158 AN: 6740

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

African (AFR) AF: 0.242 AC: 10029 AN: 41460

American (AMR) AF: 0.601 AC: 9174 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2330 AN: 5174

South Asian (SAS) AF: 0.609 AC: 2935 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7181 AN: 10560

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47399 AN: 67974

Other (OTH) AF: 0.586 AC: 1236 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3858119; hg19: chr9-80335076;