rs1060504720
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM2PM4PP3BP6_Moderate
The NM_001369387.1(GNAL):c.113_118del(p.Ala38_Lys40delinsGlu) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 32)
Consequence
GNAL
NM_001369387.1 inframe_deletion
NM_001369387.1 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.59
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_001369387.1.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
BP6
?
Variant 18-11752545-GCTTACA-G is Benign according to our data. Variant chr18-11752545-GCTTACA-G is described in ClinVar as [Benign]. Clinvar id is 416014.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNAL | NM_001369387.1 | c.113_118del | p.Ala38_Lys40delinsGlu | inframe_deletion | 1/12 | ENST00000423027.8 | |
GNAL | NM_182978.4 | c.377-307_377-302del | intron_variant | ENST00000334049.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNAL | ENST00000423027.8 | c.113_118del | p.Ala38_Lys40delinsGlu | inframe_deletion | 1/12 | 1 | NM_001369387.1 | P1 | |
GNAL | ENST00000535121.5 | c.113_118del | p.Ala38_Lys40delinsGlu | inframe_deletion | 2/13 | 1 | P1 | ||
GNAL | ENST00000334049.11 | c.377-307_377-302del | intron_variant | 1 | NM_182978.4 | ||||
GNAL | ENST00000269162.9 | c.113_118del | p.Ala38_Lys40delinsGlu | inframe_deletion | 2/13 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 08, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at