rs4745678

Positions:

• chr9-77968774-T-A
• chr9-77968774-T-C

Variant summary

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

The NM_002072.5(GNAQ):​c.137-46429A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,092 control chromosomes in the GnomAD database, including 13,141 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 0.40 (13141 hom., cov: 33)
• Consequence: GNAQ NM_002072.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GNAQ	NM_002072.5	c.137-46429A>T		intron_variant		ENST00000286548.9	NP_002063.2
GNAQ	XM_047423240.1	c.-24017A>T		5_prime_UTR_variant	1/7		XP_047279196.1
GNAQ	XM_047423239.1	c.-38-46429A>T		intron_variant			XP_047279195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GNAQ	ENST00000286548.9	c.137-46429A>T		intron_variant		1	NM_002072.5	ENSP00000286548	P1
GNAQ	ENST00000411677.1	c.50-46429A>T		intron_variant		3		ENSP00000391501

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61400 AN: 151974 Hom.: 13141 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.404 AC: 61410 AN: 152092 Hom.: 13141 Cov.: 33 AF XY: 0.402 AC XY: 29900 AN XY: 74344

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.388

Alfa AF: 0.283 Hom.: 689

Bravo AF: 0.399

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.12
DANN	Benign	0.52

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: rs4745678; hg19: chr9-80583690;