GeneBe

7-30594853-T-C

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001316772.1(GARS1):​c.-231T>C variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.0000025 in 1,200,368 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.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000025 ( 0 hom. )

Consequence

GARS1
NM_001316772.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.85
Variant links:
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]
GARS1-DT (HGNC:48951): (GARS1 divergent transcript)

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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=-0.27).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GARS1NM_001316772.1 linkc.-231T>C 5_prime_UTR_variant Exon 1 of 17 NP_001303701.1 P41250-2
GARS1NM_002047.4 linkc.-69T>C upstream_gene_variant ENST00000389266.8 NP_002038.2 P41250-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GARS1ENST00000675810 linkc.-69T>C 5_prime_UTR_variant Exon 1 of 16 ENSP00000502743.1 A0A6Q8PHH9
GARS1ENST00000674815 linkc.-247T>C 5_prime_UTR_variant Exon 1 of 17 ENSP00000502799.1 A0A6Q8PGW4
GARS1ENST00000675051.1 linkc.22-3943T>C intron_variant Intron 1 of 16 ENSP00000502296.1 A0A6Q8PGI6
GARS1ENST00000674643.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 17 ENSP00000501636.1 A0A6Q8PF45
GARS1ENST00000674807.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 16 ENSP00000502814.1 A0A6Q8PFZ6
GARS1ENST00000675529.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 18 ENSP00000501655.1 A0A6Q8PFN0
GARS1ENST00000676088.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 19 ENSP00000501884.1 A0A6Q8PFN0
GARS1ENST00000676210.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 18 ENSP00000502373.1 A0A6Q8PGN7
GARS1ENST00000676403.1 linkn.-69T>C non_coding_transcript_exon_variant Exon 1 of 16 ENSP00000502681.1 A0A6Q8PHI7
GARS1ENST00000674643.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 17 ENSP00000501636.1 A0A6Q8PF45
GARS1ENST00000674807.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 16 ENSP00000502814.1 A0A6Q8PFZ6
GARS1ENST00000675529.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 18 ENSP00000501655.1 A0A6Q8PFN0
GARS1ENST00000676088.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 19 ENSP00000501884.1 A0A6Q8PFN0
GARS1ENST00000676210.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 18 ENSP00000502373.1 A0A6Q8PGN7
GARS1ENST00000676403.1 linkn.-69T>C 5_prime_UTR_variant Exon 1 of 16 ENSP00000502681.1 A0A6Q8PHI7
GARS1ENST00000389266.8 linkc.-69T>C upstream_gene_variant 1 NM_002047.4 ENSP00000373918.3 P41250-1
GARS1ENST00000675651.1 linkc.-69T>C upstream_gene_variant ENSP00000502513.1 A0A6Q8PGZ8
GARS1ENST00000675693.1 linkc.-69T>C upstream_gene_variant ENSP00000502174.1 A0A6Q8PGA8
GARS1ENST00000674851.1 linkc.-283T>C upstream_gene_variant ENSP00000502451.1 A0A6Q8PGW4
GARS1ENST00000444666.6 linkn.-69T>C upstream_gene_variant 3 ENSP00000415447.2 H7C443
GARS1ENST00000674616.1 linkn.-69T>C upstream_gene_variant ENSP00000502408.1 A0A6Q8PGT3
GARS1ENST00000674737.1 linkn.-69T>C upstream_gene_variant ENSP00000502464.1 A0A6Q8PGZ9
GARS1ENST00000675859.1 linkn.-69T>C upstream_gene_variant ENSP00000502033.1 A0A6Q8PFZ6
GARS1ENST00000676140.1 linkn.-69T>C upstream_gene_variant ENSP00000502571.1 A0A6Q8PH49
GARS1ENST00000676164.1 linkn.-69T>C upstream_gene_variant ENSP00000501986.1 A0A6Q8PFV5
GARS1ENST00000676259.1 linkn.-69T>C upstream_gene_variant ENSP00000501980.1 A0A6Q8PFU7

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000250
AC:
3
AN:
1200368
Hom.:
0
Cov.:
17
AF XY:
0.00000167
AC XY:
1
AN XY:
600340
show subpopulations
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:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000327
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.27
CADD
Benign
18
DANN
Benign
0.88

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: chr7-30634469; API