7-30595095-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_002047.4(GARS1):c.174G>C(p.Ala58Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A58A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
GARS1
NM_002047.4 synonymous
NM_002047.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.534
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
Synonymous conserved (PhyloP=-0.534 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GARS1 | ENST00000389266.8 | c.174G>C | p.Ala58Ala | synonymous_variant | Exon 1 of 17 | 1 | NM_002047.4 | ENSP00000373918.3 | ||
| GARS1 | ENST00000675651.1 | c.174G>C | p.Ala58Ala | synonymous_variant | Exon 1 of 17 | ENSP00000502513.1 | ||||
| GARS1 | ENST00000675810.1 | c.174G>C | p.Ala58Ala | synonymous_variant | Exon 1 of 16 | ENSP00000502743.1 | ||||
| GARS1 | ENST00000444666.6 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 18 | 3 | ENSP00000415447.2 | ||||
| GARS1 | ENST00000674616.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502408.1 | |||||
| GARS1 | ENST00000674643.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501636.1 | |||||
| GARS1 | ENST00000674737.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502464.1 | |||||
| GARS1 | ENST00000674807.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 16 | ENSP00000502814.1 | |||||
| GARS1 | ENST00000675529.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000501655.1 | |||||
| GARS1 | ENST00000675859.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 15 | ENSP00000502033.1 | |||||
| GARS1 | ENST00000676088.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 19 | ENSP00000501884.1 | |||||
| GARS1 | ENST00000676140.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000502571.1 | |||||
| GARS1 | ENST00000676164.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501986.1 | |||||
| GARS1 | ENST00000676210.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502373.1 | |||||
| GARS1 | ENST00000676259.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501980.1 | |||||
| GARS1 | ENST00000676403.1 | n.174G>C | non_coding_transcript_exon_variant | Exon 1 of 16 | ENSP00000502681.1 | |||||
| GARS1 | ENST00000675693.1 | c.19-13G>C | intron_variant | Intron 1 of 17 | ENSP00000502174.1 | |||||
| GARS1 | ENST00000675051.1 | c.22-3701G>C | intron_variant | Intron 1 of 16 | ENSP00000502296.1 | |||||
| GARS1 | ENST00000674815.1 | c.-148+143G>C | intron_variant | Intron 1 of 16 | ENSP00000502799.1 | |||||
| GARS1 | ENST00000674851.1 | c.-183-13G>C | intron_variant | Intron 1 of 17 | ENSP00000502451.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390890Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 687152 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1390890
Hom.:
Cov.:
36
AF XY:
AC XY:
0
AN XY:
687152
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32026
American (AMR)
AF:
AC:
0
AN:
36548
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25212
East Asian (EAS)
AF:
AC:
0
AN:
36306
South Asian (SAS)
AF:
AC:
1
AN:
79902
European-Finnish (FIN)
AF:
AC:
0
AN:
35284
Middle Eastern (MID)
AF:
AC:
0
AN:
5644
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1081866
Other (OTH)
AF:
AC:
0
AN:
58102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
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