rs758434035

Positions:

• chr7-30595083-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_002047.4(GARS1):​c.162C>T​(p.Ser54Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,394,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: GARS1 NM_002047.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.937

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP6: Variant 7-30595083-C-T is Benign according to our data. Variant chr7-30595083-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 574424.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.937 with no splicing effect.
• BS2: High AC in GnomAdExome4 at 26 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARS1	NM_002047.4	c.162C>T	p.Ser54Ser	synonymous_variant	1/17	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1	c.-1C>T		5_prime_UTR_variant	1/17		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARS1	ENST00000389266.8	c.162C>T	p.Ser54Ser	synonymous_variant	1/17	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1	c.162C>T	p.Ser54Ser	synonymous_variant	1/17			ENSP00000502513.1
GARS1	ENST00000675810.1	c.162C>T	p.Ser54Ser	synonymous_variant	1/16			ENSP00000502743.1
GARS1	ENST00000675693.1	c.19-25C>T		intron_variant				ENSP00000502174.1
GARS1	ENST00000675051.1	c.22-3713C>T		intron_variant				ENSP00000502296.1
GARS1	ENST00000674815.1	c.-148+131C>T		intron_variant				ENSP00000502799.1
GARS1	ENST00000674851.1	c.-183-25C>T		intron_variant				ENSP00000502451.1
GARS1	ENST00000444666.6	n.162C>T		non_coding_transcript_exon_variant	1/18	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.162C>T		non_coding_transcript_exon_variant	1/18			ENSP00000502408.1
GARS1	ENST00000674643.1	n.162C>T		non_coding_transcript_exon_variant	1/17			ENSP00000501636.1
GARS1	ENST00000674737.1	n.162C>T		non_coding_transcript_exon_variant	1/18			ENSP00000502464.1
GARS1	ENST00000674807.1	n.162C>T		non_coding_transcript_exon_variant	1/16			ENSP00000502814.1
GARS1	ENST00000675529.1	n.162C>T		non_coding_transcript_exon_variant	1/18			ENSP00000501655.1
GARS1	ENST00000675859.1	n.162C>T		non_coding_transcript_exon_variant	1/15			ENSP00000502033.1
GARS1	ENST00000676088.1	n.162C>T		non_coding_transcript_exon_variant	1/19			ENSP00000501884.1
GARS1	ENST00000676140.1	n.162C>T		non_coding_transcript_exon_variant	1/17			ENSP00000502571.1
GARS1	ENST00000676164.1	n.162C>T		non_coding_transcript_exon_variant	1/17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.162C>T		non_coding_transcript_exon_variant	1/18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.162C>T		non_coding_transcript_exon_variant	1/17			ENSP00000501980.1
GARS1	ENST00000676403.1	n.162C>T		non_coding_transcript_exon_variant	1/16			ENSP00000502681.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000669 AC: 1 AN: 149544 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 81326

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000164

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000186 AC: 26 AN: 1394368 Hom.: 0 Cov.: 36 AF XY: 0.0000145 AC XY: 10 AN XY: 689206

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: 0.0000231

Gnomad4 OTH exome AF: 0.0000172

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Charcot-Marie-Tooth disease type 2 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.97
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8

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

Other links and lift over

dbSNP: rs758434035; hg19: chr7-30634699;