NM_002072.5:c.735+241G>C

Variant names:

• chr9-77794222-C-G
• rs1328530
• NM_002072.5:c.735+241G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002072.5(GNAQ):​c.735+241G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,956 control chromosomes in the GnomAD database, including 25,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.55 (25363 hom., cov: 32)
• Consequence: GNAQ NM_002072.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.539

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 9-77794222-C-G is Benign according to our data. Variant chr9-77794222-C-G is described in ClinVar as [Benign]. Clinvar id is 1286804.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 rank	MANE	Protein	UniProt
GNAQ	NM_002072.5	c.735+241G>C		intron_variant	Intron 5 of 6	ENST00000286548.9	NP_002063.2
GNAQ	XM_047423239.1	c.561+241G>C		intron_variant	Intron 5 of 6		XP_047279195.1
GNAQ	XM_047423240.1	c.561+241G>C		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	c.735+241G>C		intron_variant	Intron 5 of 6	1	NM_002072.5	ENSP00000286548.4

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83281 AN: 151838 Hom.: 25361 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.548 AC: 83306 AN: 151956 Hom.: 25363 Cov.: 32 AF XY: 0.547 AC XY: 40647 AN XY: 74258

African (AFR) AF: 0.268 AC: 11085 AN: 41434

American (AMR) AF: 0.602 AC: 9181 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2263 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2464 AN: 5160

South Asian (SAS) AF: 0.598 AC: 2885 AN: 4822

European-Finnish (FIN) AF: 0.650 AC: 6870 AN: 10564

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46447 AN: 67936

Other (OTH) AF: 0.581 AC: 1228 AN: 2112

Alfa AF: 0.474 Hom.: 1552

Bravo AF: 0.531

Asia WGS AF: 0.566 AC: 1970 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs1328530; hg19: chr9-80409138;