GeneBe

rs5898555

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_002072.5(GNAQ):​c.736-9_736-5delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000845 in 1,183,214 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 8.5e-7 ( 0 hom. )

Consequence

GNAQ
NM_002072.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.10

Publications

0 publications found
Variant links:
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

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

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.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GNAQ
NM_002072.5
MANE Select
c.736-9_736-5delTTTTT
splice_region intron
N/ANP_002063.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
GNAQ
ENST00000286548.9
TSL:1 MANE Select
c.736-9_736-5delTTTTT
splice_region intron
N/AENSP00000286548.4P50148
GNAQ
ENST00000857199.1
c.811-9_811-5delTTTTT
splice_region intron
N/AENSP00000527258.1
GNAQ
ENST00000915940.1
c.736-9_736-5delTTTTT
splice_region intron
N/AENSP00000585999.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
8.45e-7
AC:
1
AN:
1183214
Hom.:
0
AF XY:
0.00000168
AC XY:
1
AN XY:
593640
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
27000
American (AMR)
AF:
0.00
AC:
0
AN:
29394
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21322
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36630
South Asian (SAS)
AF:
0.00
AC:
0
AN:
70578
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
42924
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4560
European-Non Finnish (NFE)
AF:
0.00000111
AC:
1
AN:
900804
Other (OTH)
AF:
0.00
AC:
0
AN:
50002
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs5898555; hg19: chr9-80343587; API