9-77728671-GAA-G

Variant names:

• chr9-77728671-GAA-G
• rs5898555
• NM_002072.5:c.736-6_736-5delTT

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_002072.5(GNAQ):​c.736-6_736-5delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000511 in 1,324,040 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAd4), which may indicate mosaicism or somatic mutations in the reference population data. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.000055 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00057 (0 hom.)
• Consequence: GNAQ NM_002072.5 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.572

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: Likely_benign. The variant received -1 ACMG points.

• BP6: Variant 9-77728671-GAA-G is Benign according to our data. Variant chr9-77728671-GAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 3040162.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr9-77728671-GAA-G is described in Lovd as [Likely_benign]. Variant chr9-77728671-GAA-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAQ	NM_002072.5	c.736-6_736-5delTT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000286548.9	NP_002063.2
GNAQ	XM_047423239.1	c.562-6_562-5delTT		splice_region_variant, intron_variant	Intron 5 of 6		XP_047279195.1
GNAQ	XM_047423240.1	c.562-6_562-5delTT		splice_region_variant, 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.736-6_736-5delTT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_002072.5	ENSP00000286548.4

Frequencies

GnomAD3 genomes AF: 0.0000618 AC: 9 AN: 145624 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000216

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000462 AC: 79 AN: 170990 AF XY: 0.000415

Gnomad AFR exome AF: 0.00178

Gnomad AMR exome AF: 0.000325

Gnomad ASJ exome AF: 0.000847

Gnomad EAS exome AF: 0.000416

Gnomad FIN exome AF: 0.000956

Gnomad NFE exome AF: 0.000269

Gnomad OTH exome AF: 0.000263

GnomAD4 exome AF: 0.000568 AC: 669 AN: 1178350 Hom.: 0 AF XY: 0.000578 AC XY: 342 AN XY: 591254

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00209 AC: 56 AN: 26820

American (AMR) AF: 0.000478 AC: 14 AN: 29306

Ashkenazi Jewish (ASJ) AF: 0.000188 AC: 4 AN: 21236

East Asian (EAS) AF: 0.000412 AC: 15 AN: 36418

South Asian (SAS) AF: 0.000570 AC: 40 AN: 70220

European-Finnish (FIN) AF: 0.000842 AC: 36 AN: 42734

Middle Eastern (MID) AF: 0.000220 AC: 1 AN: 4538

European-Non Finnish (NFE) AF: 0.000525 AC: 471 AN: 897258

Other (OTH) AF: 0.000642 AC: 32 AN: 49820

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000549 AC: 8 AN: 145690 Hom.: 0 Cov.: 0 AF XY: 0.0000708 AC XY: 5 AN XY: 70618

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000177 AC: 7 AN: 39616

American (AMR) AF: 0.00 AC: 0 AN: 14696

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3420

East Asian (EAS) AF: 0.00 AC: 0 AN: 4934

South Asian (SAS) AF: 0.000217 AC: 1 AN: 4616

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8728

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 276

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66490

Other (OTH) AF: 0.00 AC: 0 AN: 2008

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.001767), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

GNAQ-related disorder Benign:1

Oct 28, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.57

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

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Other links and lift over

dbSNP: rs5898555; hg19: chr9-80343587;