rs200887429
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_002047.4(GARS1):c.302G>A(p.Arg101His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R101C) has been classified as Likely benign.
Frequency
Consequence
NM_002047.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GARS1 | NM_002047.4 | c.302G>A | p.Arg101His | missense_variant | 2/17 | ENST00000389266.8 | |
GARS1 | NM_001316772.1 | c.140G>A | p.Arg47His | missense_variant | 2/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARS1 | ENST00000389266.8 | c.302G>A | p.Arg101His | missense_variant | 2/17 | 1 | NM_002047.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000345 AC: 86AN: 249370Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135338
GnomAD4 exome AF: 0.000274 AC: 401AN: 1461678Hom.: 0 Cov.: 31 AF XY: 0.000267 AC XY: 194AN XY: 727146
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74476
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | GARS1: BS2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 17, 2022 | Reported as a variant of unknown significance in individuals tested by an outside laboratory suspected of having Charcot-Marie-Tooth disease (DiVincenzo et al., 2014; Nam et al., 2021; Volodarsky et al., 2021); Identified previously in the heterozygous state in two individuals with neuropathy (Antoniadi et al., 2015; Apellniz-Ruiz et al., 2017); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27582484, 28166811, 34813128, 32028661, 34426522, 29520015, 32376792, 25614874, 26392352) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 29, 2021 | - - |
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 17, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 21, 2024 | Variant summary: GARS1 c.302G>A (p.Arg101His) results in a non-conservative amino acid change located in the WHEP-TRS domain (IPR000738) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00031 in 280760 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.302G>A has been reported in the literature in individuals affected with neuropathy, CMT, or ALS without strong evidence of causality (e.g. Antoniadi_2015, Apellaniz-Ruiz_2017, Pensato_2020, Volodarsky_2021, Nam_2022). These reports do not provide unequivocal conclusions about association of the variant with GARS1-Related Disorders. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant does not result in aberrant GlyRS-HDAC6 interaction (Mo_2018). The following publications have been ascertained in the context of this evaluation (PMID: 26392352, 27582484, 29520015, 32028661, 32376792, 34813128). ClinVar contains an entry for this variant (Variation ID: 245685). Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Distal spinal muscular atrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Charcot-Marie-Tooth disease type 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Charcot-Marie-Tooth disease type 2D Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Neuronopathy, distal hereditary motor, type 5A Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at