rs5898555

Variant names:

• chr9-77728671-GAAA-G
• NM_002072.5:c.736-7_736-5delTTT

Your query was ambiguous. Multiple possible variants found:

• chr9-77728671-GAAA-G
• chr9-77728671-GAAA-GA
• chr9-77728671-GAAA-GAA
• chr9-77728671-GAAA-GAAAA
• chr9-77728671-GAAA-GAAAAA
• chr9-77728671-GAAA-GAAAAAA
• chr9-77728671-GAAA-GAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_002072.5(GNAQ):​c.736-7_736-5delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,182,650 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000036 (0 hom.)
• Consequence: GNAQ NM_002072.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 42 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAQ	NM_002072.5	c.736-7_736-5delTTT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000286548.9	NP_002063.2
GNAQ	XM_047423239.1	c.562-7_562-5delTTT		splice_region_variant, intron_variant	Intron 5 of 6		XP_047279195.1
GNAQ	XM_047423240.1	c.562-7_562-5delTTT		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.736-7_736-5delTTT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_002072.5	ENSP00000286548.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000355 AC: 42 AN: 1182650 Hom.: 0 AF XY: 0.0000354 AC XY: 21 AN XY: 593378

Gnomad4 AFR exome AF: 0.0000741

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000567

Gnomad4 FIN exome AF: 0.0000699

Gnomad4 NFE exome AF: 0.0000355

Gnomad4 OTH exome AF: 0.0000200

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-80343587;