NM_002047.4(GARS1):c.882-15T>G AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jan 16, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_002047.4(GARS1):c.882-15T>G]


GARS1:glycyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000007.14:g.30612081T>G
  • NG_007942.1:g.22517T>G
  • NM_001316772.1:c.720-15T>G
  • NM_002047.4:c.882-15T>GMANE SELECT
  • LRG_243t1:c.882-15T>G
  • LRG_243:g.22517T>G
  • NC_000007.13:g.30651697T>G
  • NM_002047.2:c.882-15T>G
dbSNP: rs199741850
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001316772.1:c.720-15T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002047.4:c.882-15T>G - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000535770GeneDxcriteria provided, single submitter
Uncertain significance
(Jan 16, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000535770.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


The c.882-15 T>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.882-15 T>G variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The Exome Aggregation Consortium (ExAC) database reports c.882-15 T>G was observed in 15/16492 alleles from individuals of South Asian background. This substitution occurs at a position that is not conserved. Several in-silico splice prediction models predict that c.882-15 T>G creates a cryptic acceptor site which may supplant the natural acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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