rs752464405

Variant names:

• chr7-30628597-C-G
• NM_002047.4:c.1737C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-30628597-C-G
• chr7-30628597-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_002047.4(GARS1):​c.1737C>G​(p.Phe579Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: GARS1 NM_002047.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.943

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARS1	NM_002047.4	c.1737C>G	p.Phe579Leu	missense_variant	Exon 14 of 17	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1	c.1575C>G	p.Phe525Leu	missense_variant	Exon 14 of 17		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARS1	ENST00000389266.8	c.1737C>G	p.Phe579Leu	missense_variant	Exon 14 of 17	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1	c.1737C>G	p.Phe579Leu	missense_variant	Exon 14 of 17			ENSP00000502513.1
GARS1	ENST00000675810.1	c.1635C>G	p.Phe545Leu	missense_variant	Exon 13 of 16			ENSP00000502743.1
GARS1	ENST00000675693.1	c.1569C>G	p.Phe523Leu	missense_variant	Exon 15 of 18			ENSP00000502174.1
GARS1	ENST00000675051.1	c.1536C>G	p.Phe512Leu	missense_variant	Exon 14 of 17			ENSP00000502296.1
GARS1	ENST00000674815.1	c.1368C>G	p.Phe456Leu	missense_variant	Exon 14 of 17			ENSP00000502799.1
GARS1	ENST00000674851.1	c.1368C>G	p.Phe456Leu	missense_variant	Exon 15 of 18			ENSP00000502451.1
GARS1	ENST00000444666.6	n.*158C>G		non_coding_transcript_exon_variant	Exon 15 of 18	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.*1451C>G		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502408.1
GARS1	ENST00000674643.1	n.*837C>G		non_coding_transcript_exon_variant	Exon 15 of 17			ENSP00000501636.1
GARS1	ENST00000674737.1	n.*1075C>G		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502464.1
GARS1	ENST00000674807.1	n.*10C>G		non_coding_transcript_exon_variant	Exon 13 of 16			ENSP00000502814.1
GARS1	ENST00000675529.1	n.*1607C>G		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000501655.1
GARS1	ENST00000675859.1	n.*10C>G		non_coding_transcript_exon_variant	Exon 13 of 15			ENSP00000502033.1
GARS1	ENST00000676088.1	n.*1679C>G		non_coding_transcript_exon_variant	Exon 16 of 19			ENSP00000501884.1
GARS1	ENST00000676140.1	n.*682C>G		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000502571.1
GARS1	ENST00000676164.1	n.*1188C>G		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.*1026C>G		non_coding_transcript_exon_variant	Exon 15 of 18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.*1169C>G		non_coding_transcript_exon_variant	Exon 14 of 17			ENSP00000501980.1
GARS1	ENST00000676403.1	n.1737C>G		non_coding_transcript_exon_variant	Exon 14 of 16			ENSP00000502681.1
GARS1	ENST00000444666.6	n.*158C>G		3_prime_UTR_variant	Exon 15 of 18	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.*1451C>G		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502408.1
GARS1	ENST00000674643.1	n.*837C>G		3_prime_UTR_variant	Exon 15 of 17			ENSP00000501636.1
GARS1	ENST00000674737.1	n.*1075C>G		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502464.1
GARS1	ENST00000674807.1	n.*10C>G		3_prime_UTR_variant	Exon 13 of 16			ENSP00000502814.1
GARS1	ENST00000675529.1	n.*1607C>G		3_prime_UTR_variant	Exon 15 of 18			ENSP00000501655.1
GARS1	ENST00000675859.1	n.*10C>G		3_prime_UTR_variant	Exon 13 of 15			ENSP00000502033.1
GARS1	ENST00000676088.1	n.*1679C>G		3_prime_UTR_variant	Exon 16 of 19			ENSP00000501884.1
GARS1	ENST00000676140.1	n.*682C>G		3_prime_UTR_variant	Exon 14 of 17			ENSP00000502571.1
GARS1	ENST00000676164.1	n.*1188C>G		3_prime_UTR_variant	Exon 14 of 17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.*1026C>G		3_prime_UTR_variant	Exon 15 of 18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.*1169C>G		3_prime_UTR_variant	Exon 14 of 17			ENSP00000501980.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460646 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 726614

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: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.36
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.67	D
Eigen	Benign	-0.084
Eigen_PC	Benign	-0.16
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Pathogenic	0.48	D
MetaRNN	Pathogenic	0.94	D
MetaSVM	Uncertain	0.52	D
PrimateAI	Pathogenic	0.80	D
PROVEAN	Pathogenic	-5.8	D
REVEL	Pathogenic	0.79
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.83
MutPred		0.72		Gain of loop (P = 0.2754);
MVP		0.94
MPC		1.2
ClinPred		0.99	D
GERP RS		-0.79
Varity_R		0.97
gMVP		0.76

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: chr7-30668213;