GeneBe

rs5898555

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 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
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNAQNM_002072.5 linkc.736-9_736-5delTTTTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000286548.9 NP_002063.2 P50148A0A024R240
GNAQXM_047423239.1 linkc.562-9_562-5delTTTTT splice_region_variant, intron_variant Intron 5 of 6 XP_047279195.1
GNAQXM_047423240.1 linkc.562-9_562-5delTTTTT 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
GNAQENST00000286548.9 linkc.736-9_736-5delTTTTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_002072.5 ENSP00000286548.4 P50148

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
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000111
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-80343587; API