NM_002047.4:c.2145A>G

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002047.4(GARS1):c.2145A>G(p.Thr715Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 1,608,902 control chromosomes in the GnomAD database, including 2,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.084 ( 1155 hom., cov: 31)

Exomes 𝑓: 0.035 ( 1684 hom. )

Consequence

GARS1
NM_002047.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -1.72

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 7-30633785-A-G is Benign according to our data. Variant chr7-30633785-A-G is described in ClinVar as [Benign]. Clinvar id is 137443.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-30633785-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.72 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARS1	NM_002047.4 link	c.2145A>G	p.Thr715Thr	synonymous_variant	Exon 17 of 17	ENST00000389266.8	NP_002038.2	P41250-1
GARS1	NM_001316772.1 link	c.1983A>G	p.Thr661Thr	synonymous_variant	Exon 17 of 17		NP_001303701.1	P41250-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GARS1	ENST00000389266.8 link	c.2145A>G	p.Thr715Thr	synonymous_variant	Exon 17 of 17	1	NM_002047.4	ENSP00000373918.3	P41250-1
GARS1	ENST00000675651.1 link	c.2163A>G	p.Thr721Thr	synonymous_variant	Exon 17 of 17			ENSP00000502513.1	A0A6Q8PGZ8
GARS1	ENST00000675810.1 link	c.2043A>G	p.Thr681Thr	synonymous_variant	Exon 16 of 16			ENSP00000502743.1	A0A6Q8PHH9
GARS1	ENST00000675693.1 link	c.1977A>G	p.Thr659Thr	synonymous_variant	Exon 18 of 18			ENSP00000502174.1	A0A6Q8PGA8
GARS1	ENST00000675051.1 link	c.1944A>G	p.Thr648Thr	synonymous_variant	Exon 17 of 17			ENSP00000502296.1	A0A6Q8PGI6
GARS1	ENST00000674815.1 link	c.1776A>G	p.Thr592Thr	synonymous_variant	Exon 17 of 17			ENSP00000502799.1	A0A6Q8PGW4
GARS1	ENST00000674851.1 link	c.1776A>G	p.Thr592Thr	synonymous_variant	Exon 18 of 18			ENSP00000502451.1	A0A6Q8PGW4
GARS1	ENST00000444666.6 link	n.*566A>G		non_coding_transcript_exon_variant	Exon 18 of 18	3		ENSP00000415447.2	H7C443
GARS1	ENST00000674616.1 link	n.*1859A>G		non_coding_transcript_exon_variant	Exon 18 of 18			ENSP00000502408.1	A0A6Q8PGT3
GARS1	ENST00000674643.1 link	n.*1950A>G		non_coding_transcript_exon_variant	Exon 17 of 17			ENSP00000501636.1	A0A6Q8PF45
GARS1	ENST00000674737.1 link	n.*1483A>G		non_coding_transcript_exon_variant	Exon 18 of 18			ENSP00000502464.1	A0A6Q8PGZ9
GARS1	ENST00000674807.1 link	n.*418A>G		non_coding_transcript_exon_variant	Exon 16 of 16			ENSP00000502814.1	A0A6Q8PFZ6
GARS1	ENST00000675529.1 link	n.*2015A>G		non_coding_transcript_exon_variant	Exon 18 of 18			ENSP00000501655.1	A0A6Q8PFN0
GARS1	ENST00000675859.1 link	n.*324A>G		non_coding_transcript_exon_variant	Exon 15 of 15			ENSP00000502033.1	A0A6Q8PFZ6
GARS1	ENST00000676088.1 link	n.*2087A>G		non_coding_transcript_exon_variant	Exon 19 of 19			ENSP00000501884.1	A0A6Q8PFN0
GARS1	ENST00000676140.1 link	n.*1090A>G		non_coding_transcript_exon_variant	Exon 17 of 17			ENSP00000502571.1	A0A6Q8PH49
GARS1	ENST00000676164.1 link	n.*1596A>G		non_coding_transcript_exon_variant	Exon 17 of 17			ENSP00000501986.1	A0A6Q8PFV5
GARS1	ENST00000676210.1 link	n.*1434A>G		non_coding_transcript_exon_variant	Exon 18 of 18			ENSP00000502373.1	A0A6Q8PGN7
GARS1	ENST00000676259.1 link	n.*1577A>G		non_coding_transcript_exon_variant	Exon 17 of 17			ENSP00000501980.1	A0A6Q8PFU7
GARS1	ENST00000676403.1 link	n.*230A>G		non_coding_transcript_exon_variant	Exon 16 of 16			ENSP00000502681.1	A0A6Q8PHI7
GARS1	ENST00000444666.6 link	n.*566A>G		3_prime_UTR_variant	Exon 18 of 18	3		ENSP00000415447.2	H7C443
GARS1	ENST00000674616.1 link	n.*1859A>G		3_prime_UTR_variant	Exon 18 of 18			ENSP00000502408.1	A0A6Q8PGT3
GARS1	ENST00000674643.1 link	n.*1950A>G		3_prime_UTR_variant	Exon 17 of 17			ENSP00000501636.1	A0A6Q8PF45
GARS1	ENST00000674737.1 link	n.*1483A>G		3_prime_UTR_variant	Exon 18 of 18			ENSP00000502464.1	A0A6Q8PGZ9
GARS1	ENST00000674807.1 link	n.*418A>G		3_prime_UTR_variant	Exon 16 of 16			ENSP00000502814.1	A0A6Q8PFZ6
GARS1	ENST00000675529.1 link	n.*2015A>G		3_prime_UTR_variant	Exon 18 of 18			ENSP00000501655.1	A0A6Q8PFN0
GARS1	ENST00000675859.1 link	n.*324A>G		3_prime_UTR_variant	Exon 15 of 15			ENSP00000502033.1	A0A6Q8PFZ6
GARS1	ENST00000676088.1 link	n.*2087A>G		3_prime_UTR_variant	Exon 19 of 19			ENSP00000501884.1	A0A6Q8PFN0
GARS1	ENST00000676140.1 link	n.*1090A>G		3_prime_UTR_variant	Exon 17 of 17			ENSP00000502571.1	A0A6Q8PH49
GARS1	ENST00000676164.1 link	n.*1596A>G		3_prime_UTR_variant	Exon 17 of 17			ENSP00000501986.1	A0A6Q8PFV5
GARS1	ENST00000676210.1 link	n.*1434A>G		3_prime_UTR_variant	Exon 18 of 18			ENSP00000502373.1	A0A6Q8PGN7
GARS1	ENST00000676259.1 link	n.*1577A>G		3_prime_UTR_variant	Exon 17 of 17			ENSP00000501980.1	A0A6Q8PFU7
GARS1	ENST00000676403.1 link	n.*230A>G		3_prime_UTR_variant	Exon 16 of 16			ENSP00000502681.1	A0A6Q8PHI7

Frequencies

GnomAD3 genomes

AF:

0.0842

AC:

12779

AN:

151840

Hom.:

1146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.0512

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.000581

Gnomad SAS

AF:

0.00479

Gnomad FIN

AF:

0.0123

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0325

Gnomad OTH

AF:

0.0680

GnomAD3 exomes

AF:

0.0362

AC:

9044

AN:

249520

Hom.:

524

AF XY:

0.0329

AC XY:

4453

AN XY:

135374

show subpopulations

Gnomad AFR exome

AF:

0.225

Gnomad AMR exome

AF:

0.0280

Gnomad ASJ exome

AF:

0.0255

Gnomad EAS exome

AF:

0.000278

Gnomad SAS exome

AF:

0.00778

Gnomad FIN exome

AF:

0.0133

Gnomad NFE exome

AF:

0.0318

Gnomad OTH exome

AF:

0.0340

GnomAD4 exome

AF:

0.0353

AC:

51393

AN:

1456946

Hom.:

1684

Cov.:

AF XY:

0.0340

AC XY:

24607

AN XY:

724742

show subpopulations

Gnomad4 AFR exome

AF:

0.234

Gnomad4 AMR exome

AF:

0.0317

Gnomad4 ASJ exome

AF:

0.0243

Gnomad4 EAS exome

AF:

0.000152

Gnomad4 SAS exome

AF:

0.00831

Gnomad4 FIN exome

AF:

0.0140

Gnomad4 NFE exome

AF:

0.0335

Gnomad4 OTH exome

AF:

0.0443

GnomAD4 genome

AF:

0.0844

AC:

12819

AN:

151956

Hom.:

1155

Cov.:

AF XY:

0.0820

AC XY:

6090

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.0510

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.000582

Gnomad4 SAS

AF:

0.00501

Gnomad4 FIN

AF:

0.0123

Gnomad4 NFE

AF:

0.0325

Gnomad4 OTH

AF:

0.0673

Alfa

AF:

0.0366

Hom.:

106

Bravo

AF:

0.0945

Asia WGS

AF:

0.0210

AC:

AN:

3478

EpiCase

AF:

0.0358

EpiControl

AF:

0.0337

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 28, 2014

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. -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

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 13, 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 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Feb 29, 2016

Mayo Clinic Laboratories, Mayo Clinic

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Charcot-Marie-Tooth disease type 2D

Benign:1

Jan 13, 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 13, 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

-0.65

CADD

Benign

0.57

DANN

Benign

0.70

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over