rs779605505

Variant names:

• chr18-11689809-TGCCGAGGAGCGCGAGGCG-T
• NM_182978.4:c.250_267delGAGGAGCGCGAGGCGGCC

Your query was ambiguous. Multiple possible variants found:

• chr18-11689809-TGCCGAGGAGCGCGAGGCG-T
• chr18-11689809-TGCCGAGGAGCGCGAGGCG-TGCCGAGGAGCGCGAGGCGGCCGAGGAGCGCGAGGCG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_182978.4(GNAL):​c.250_267delGAGGAGCGCGAGGCGGCC​(p.Glu84_Ala89del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000000721 in 1,386,132 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E84E) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: GNAL NM_182978.4 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.46

Genes affected

GNAL (HGNC:4388): (G protein subunit alpha L) This gene encodes a stimulatory G protein alpha subunit which mediates odorant signaling in the olfactory epithelium. This protein couples dopamine type 1 receptors and adenosine A2A receptors and is widely expressed in the central nervous system. Mutations in this gene have been associated with dystonia 25 and this gene is located in a susceptibility region for bipolar disorder and schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_182978.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNAL	NM_182978.4	c.250_267delGAGGAGCGCGAGGCGGCC	p.Glu84_Ala89del	conservative_inframe_deletion	Exon 1 of 12	ENST00000334049.11	NP_892023.1
GNAL	XM_006722324.4	c.250_267delGAGGAGCGCGAGGCGGCC	p.Glu84_Ala89del	conservative_inframe_deletion	Exon 1 of 6		XP_006722387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNAL	ENST00000334049.11	c.250_267delGAGGAGCGCGAGGCGGCC	p.Glu84_Ala89del	conservative_inframe_deletion	Exon 1 of 12	1	NM_182978.4	ENSP00000334051.5
GNAL	ENST00000585590.1	n.124_141delGAGGAGCGCGAGGCGGCC		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.21e-7 AC: 1 AN: 1386132 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 685702

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: 0.0000128

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: chr18-11689808;