chr7-30594877-C-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000675810(GARS1):c.-45C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
GARS1
ENST00000675810 5_prime_UTR
ENST00000675810 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.351
Genes affected
GARS1 (HGNC:4162): (glycyl-tRNA synthetase 1) This gene encodes glycyl-tRNA synthetase, one of the aminoacyl-tRNA synthetases that charge tRNAs with their cognate amino acids. The encoded enzyme is an (alpha)2 dimer which belongs to the class II family of tRNA synthetases. It has been shown to be a target of autoantibodies in the human autoimmune diseases, polymyositis or dermatomyositis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GARS1 | NM_001316772.1 | c.-207C>G | 5_prime_UTR_variant | 1/17 | NP_001303701.1 | |||
| GARS1 | NM_002047.4 | c.-45C>G | upstream_gene_variant | ENST00000389266.8 | NP_002038.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GARS1 | ENST00000675810 | c.-45C>G | 5_prime_UTR_variant | 1/16 | ENSP00000502743.1 | |||||
| GARS1 | ENST00000674815 | c.-223C>G | 5_prime_UTR_variant | 1/17 | ENSP00000502799.1 | |||||
| GARS1 | ENST00000675051.1 | c.22-3919C>G | intron_variant | ENSP00000502296.1 | ||||||
| GARS1 | ENST00000674643.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/17 | ENSP00000501636.1 | |||||
| GARS1 | ENST00000674807.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/16 | ENSP00000502814.1 | |||||
| GARS1 | ENST00000675529.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/18 | ENSP00000501655.1 | |||||
| GARS1 | ENST00000676088.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/19 | ENSP00000501884.1 | |||||
| GARS1 | ENST00000676210.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/18 | ENSP00000502373.1 | |||||
| GARS1 | ENST00000676403.1 | n.-45C>G | non_coding_transcript_exon_variant | 1/16 | ENSP00000502681.1 | |||||
| GARS1 | ENST00000674643.1 | n.-45C>G | 5_prime_UTR_variant | 1/17 | ENSP00000501636.1 | |||||
| GARS1 | ENST00000674807.1 | n.-45C>G | 5_prime_UTR_variant | 1/16 | ENSP00000502814.1 | |||||
| GARS1 | ENST00000675529.1 | n.-45C>G | 5_prime_UTR_variant | 1/18 | ENSP00000501655.1 | |||||
| GARS1 | ENST00000676088.1 | n.-45C>G | 5_prime_UTR_variant | 1/19 | ENSP00000501884.1 | |||||
| GARS1 | ENST00000676210.1 | n.-45C>G | 5_prime_UTR_variant | 1/18 | ENSP00000502373.1 | |||||
| GARS1 | ENST00000676403.1 | n.-45C>G | 5_prime_UTR_variant | 1/16 | ENSP00000502681.1 | |||||
| GARS1 | ENST00000389266.8 | c.-45C>G | upstream_gene_variant | 1 | NM_002047.4 | ENSP00000373918.3 | ||||
| GARS1 | ENST00000675651.1 | c.-45C>G | upstream_gene_variant | ENSP00000502513.1 | ||||||
| GARS1 | ENST00000675693.1 | c.-45C>G | upstream_gene_variant | ENSP00000502174.1 | ||||||
| GARS1 | ENST00000674851.1 | c.-259C>G | upstream_gene_variant | ENSP00000502451.1 | ||||||
| GARS1 | ENST00000444666.6 | n.-45C>G | upstream_gene_variant | 3 | ENSP00000415447.2 | |||||
| GARS1 | ENST00000674616.1 | n.-45C>G | upstream_gene_variant | ENSP00000502408.1 | ||||||
| GARS1 | ENST00000674737.1 | n.-45C>G | upstream_gene_variant | ENSP00000502464.1 | ||||||
| GARS1 | ENST00000675859.1 | n.-45C>G | upstream_gene_variant | ENSP00000502033.1 | ||||||
| GARS1 | ENST00000676140.1 | n.-45C>G | upstream_gene_variant | ENSP00000502571.1 | ||||||
| GARS1 | ENST00000676164.1 | n.-45C>G | upstream_gene_variant | ENSP00000501986.1 | ||||||
| GARS1 | ENST00000676259.1 | n.-45C>G | upstream_gene_variant | ENSP00000501980.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 23
GnomAD4 exome
Cov.:
23
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Charcot-Marie-Tooth disease type 2D;CN031873:Neuronopathy, distal hereditary motor, type 5A Other:1
| not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at