7-30612092-A-T

Variant names:

• chr7-30612092-A-T
• rs778219649
• NM_002047.4:c.882-4A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002047.4(GARS1):​c.882-4A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: GARS1 NM_002047.4 splice_region, intron
• Scores: Splicing: ADA: 0.00009972
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 0 publications found

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARS1	NM_002047.4	c.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 16	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1	c.720-4A>T		splice_region_variant, intron_variant	Intron 7 of 16		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARS1	ENST00000389266.8	c.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 16	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1	c.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000502513.1
GARS1	ENST00000675810.1	c.780-4A>T		splice_region_variant, intron_variant	Intron 6 of 15			ENSP00000502743.1
GARS1	ENST00000675693.1	c.714-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000502174.1
GARS1	ENST00000675051.1	c.681-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000502296.1
GARS1	ENST00000674815.1	c.513-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000502799.1
GARS1	ENST00000674851.1	c.513-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000502451.1
GARS1	ENST00000444666.6	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 17	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.*596-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000502408.1
GARS1	ENST00000674643.1	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000501636.1
GARS1	ENST00000674737.1	n.*220-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000502464.1
GARS1	ENST00000674807.1	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 15			ENSP00000502814.1
GARS1	ENST00000675529.1	n.*752-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000501655.1
GARS1	ENST00000675859.1	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 14			ENSP00000502033.1
GARS1	ENST00000676088.1	n.*824-4A>T		splice_region_variant, intron_variant	Intron 9 of 18			ENSP00000501884.1
GARS1	ENST00000676140.1	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000502571.1
GARS1	ENST00000676164.1	n.*333-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000501986.1
GARS1	ENST00000676210.1	n.*171-4A>T		splice_region_variant, intron_variant	Intron 8 of 17			ENSP00000502373.1
GARS1	ENST00000676259.1	n.*314-4A>T		splice_region_variant, intron_variant	Intron 7 of 16			ENSP00000501980.1
GARS1	ENST00000676403.1	n.882-4A>T		splice_region_variant, intron_variant	Intron 7 of 15			ENSP00000502681.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1459870 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726432

African (AFR) AF: 0.00 AC: 0 AN: 33446

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26122

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39674

South Asian (SAS) AF: 0.00 AC: 0 AN: 86208

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1110196

Other (OTH) AF: 0.00 AC: 0 AN: 60320

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.51

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00010
dbscSNV1_RF	Benign	0.010
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

Other links and lift over

dbSNP: rs778219649; hg19: chr7-30651708;