chr7-30594388-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000675051.1(GARS1):​c.22-4408T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,038 control chromosomes in the GnomAD database, including 21,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 21547 hom., cov: 32)

Consequence

GARS1
ENST00000675051.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.251
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-DT (HGNC:48951): (GARS1 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 7-30594388-T-C is Benign according to our data. Variant chr7-30594388-T-C is described in ClinVar as [Benign]. Clinvar id is 683987.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GARS1ENST00000675051.1 linkuse as main transcriptc.22-4408T>C intron_variant
GARS1-DTENST00000426529.6 linkuse as main transcriptn.33+323A>G intron_variant, non_coding_transcript_variant 5
GARS1-DTENST00000578994.5 linkuse as main transcriptn.99+323A>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.487
AC:
74033
AN:
151918
Hom.:
21550
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.155
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.536
Gnomad ASJ
AF:
0.682
Gnomad EAS
AF:
0.478
Gnomad SAS
AF:
0.415
Gnomad FIN
AF:
0.642
Gnomad MID
AF:
0.560
Gnomad NFE
AF:
0.648
Gnomad OTH
AF:
0.518
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.487
AC:
74034
AN:
152038
Hom.:
21547
Cov.:
32
AF XY:
0.484
AC XY:
35959
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.154
Gnomad4 AMR
AF:
0.536
Gnomad4 ASJ
AF:
0.682
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.416
Gnomad4 FIN
AF:
0.642
Gnomad4 NFE
AF:
0.648
Gnomad4 OTH
AF:
0.515
Alfa
AF:
0.580
Hom.:
8344
Bravo
AF:
0.465
Asia WGS
AF:
0.413
AC:
1437
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018This 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
3.3
DANN
Benign
0.61

Splicing

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.

Other links and lift over

dbSNP: rs2270025; hg19: chr7-30634004; API