rs3886641

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_002047.4(GARS1):c.1761G>A(p.Thr587Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00273 in 1,612,726 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 54 hom., cov: 32)

Exomes 𝑓: 0.0015 ( 59 hom. )

Consequence

GARS1
NM_002047.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -2.18

Publications

4 publications found

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 Gene-Disease associations (from GenCC):

Charcot-Marie-Tooth disease type 2D
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet
neuronopathy, distal hereditary motor, type 5A
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Illumina, Laboratory for Molecular Medicine
spinal muscular atrophy, infantile, James type
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

GARS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 7-30628621-G-A is Benign according to our data. Variant chr7-30628621-G-A is described in ClinVar as Benign. ClinVar VariationId is 360015.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.18 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARS1	NM_002047.4 link	c.1761G>A	p.Thr587Thr	synonymous_variant	Exon 14 of 17	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1 link	c.1599G>A	p.Thr533Thr	synonymous_variant	Exon 14 of 17		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
GARS1	ENST00000389266.8 link	c.1761G>A	p.Thr587Thr	synonymous_variant	Exon 14 of 17	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1 link	c.1761G>A	p.Thr587Thr	synonymous_variant	Exon 14 of 17			ENSP00000502513.1
GARS1	ENST00000675810.1 link	c.1659G>A	p.Thr553Thr	synonymous_variant	Exon 13 of 16			ENSP00000502743.1
GARS1	ENST00000675693.1 link	c.1593G>A	p.Thr531Thr	synonymous_variant	Exon 15 of 18			ENSP00000502174.1
GARS1	ENST00000675051.1 link	c.1560G>A	p.Thr520Thr	synonymous_variant	Exon 14 of 17			ENSP00000502296.1
GARS1	ENST00000674815.1 link	c.1392G>A	p.Thr464Thr	synonymous_variant	Exon 14 of 17			ENSP00000502799.1
GARS1	ENST00000674851.1 link	c.1392G>A	p.Thr464Thr	synonymous_variant	Exon 15 of 18			ENSP00000502451.1
GARS1	ENST00000444666.6 link	n.*182G>A		non_coding_transcript_exon_variant	Exon 15 of 18	3		ENSP00000415447.2
GARS1	ENST00000674616.1 link	n.*1475G>A		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502408.1
GARS1	ENST00000674643.1 link	n.*861G>A		non_coding_transcript_exon_variant	Exon 15 of 17			ENSP00000501636.1
GARS1	ENST00000674737.1 link	n.*1099G>A		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502464.1
GARS1	ENST00000674807.1 link	n.*34G>A		non_coding_transcript_exon_variant	Exon 13 of 16			ENSP00000502814.1
GARS1	ENST00000675529.1 link	n.*1631G>A		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000501655.1
GARS1	ENST00000675859.1 link	n.*34G>A		non_coding_transcript_exon_variant	Exon 13 of 15			ENSP00000502033.1
GARS1	ENST00000676088.1 link	n.*1703G>A		non_coding_transcript_exon_variant	Exon 16 of 19			ENSP00000501884.1
GARS1	ENST00000676140.1 link	n.*706G>A		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000502571.1
GARS1	ENST00000676164.1 link	n.*1212G>A		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000501986.1
GARS1	ENST00000676210.1 link	n.*1050G>A		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502373.1
GARS1	ENST00000676259.1 link	n.*1193G>A		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000501980.1
GARS1	ENST00000676403.1 link	n.1761G>A		non_coding_transcript_exon_variant	Exon 14 of 16			ENSP00000502681.1
GARS1	ENST00000444666.6 link	n.*182G>A		3_prime_UTR_variant	Exon 15 of 18	3		ENSP00000415447.2
GARS1	ENST00000674616.1 link	n.*1475G>A		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502408.1
GARS1	ENST00000674643.1 link	n.*861G>A		3_prime_UTR_variant	Exon 15 of 17			ENSP00000501636.1
GARS1	ENST00000674737.1 link	n.*1099G>A		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502464.1
GARS1	ENST00000674807.1 link	n.*34G>A		3_prime_UTR_variant	Exon 13 of 16			ENSP00000502814.1
GARS1	ENST00000675529.1 link	n.*1631G>A		3_prime_UTR_variant	Exon 15 of 18			ENSP00000501655.1
GARS1	ENST00000675859.1 link	n.*34G>A		3_prime_UTR_variant	Exon 13 of 15			ENSP00000502033.1
GARS1	ENST00000676088.1 link	n.*1703G>A		3_prime_UTR_variant	Exon 16 of 19			ENSP00000501884.1
GARS1	ENST00000676140.1 link	n.*706G>A		3_prime_UTR_variant	Exon 14 of 17			ENSP00000502571.1
GARS1	ENST00000676164.1 link	n.*1212G>A		3_prime_UTR_variant	Exon 14 of 17			ENSP00000501986.1
GARS1	ENST00000676210.1 link	n.*1050G>A		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502373.1
GARS1	ENST00000676259.1 link	n.*1193G>A		3_prime_UTR_variant	Exon 14 of 17			ENSP00000501980.1

Frequencies

GnomAD3 genomes

AF:

0.0141

AC:

2144

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0486

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.00814

GnomAD2 exomes

AF:

0.00395

AC:

986

AN:

249570

AF XY:

0.00284

show subpopulations

Gnomad AFR exome

AF:

0.0531

Gnomad AMR exome

AF:

0.00336

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000115

Gnomad OTH exome

AF:

0.00148

GnomAD4 exome

AF:

0.00154

AC:

2250

AN:

1460498

Hom.:

Cov.:

AF XY:

0.00140

AC XY:

1019

AN XY:

726578

show subpopulations

African (AFR)

AF:

0.0521

AC:

1743

AN:

33442

American (AMR)

AF:

0.00338

AC:

151

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26082

East Asian (EAS)

AF:

0.00

AC:

AN:

39660

South Asian (SAS)

AF:

0.000707

AC:

AN:

86232

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53380

Middle Eastern (MID)

AF:

0.00226

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.0000747

AC:

AN:

1110916

Other (OTH)

AF:

0.00330

AC:

199

AN:

60328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

111

221

332

442

553

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

192

256

320

<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

AF:

0.0141

AC:

2145

AN:

152228

Hom.:

Cov.:

AF XY:

0.0135

AC XY:

1008

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0485

AC:

2015

AN:

41530

American (AMR)

AF:

0.00588

AC:

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.000829

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10594

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000250

AC:

AN:

68010

Other (OTH)

AF:

0.00806

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

107

213

320

426

533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00717

Hom.:

Bravo

AF:

0.0164

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000237

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Feb 22, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Jun 27, 2024

Athena Diagnostics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Charcot-Marie-Tooth disease

Benign:1

Molecular Genetics Laboratory, London Health Sciences Centre

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Distal spinal muscular atrophy

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Mar 31, 2022

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Charcot-Marie-Tooth disease type 2D

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Neuronopathy, distal hereditary motor, type 5A

Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

1.3

(source)

DANN

Benign

0.76

PhyloP100

-2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over