NM_012208.3(HARS2):c.7C>G (p.Leu3Val)

Variation ID: Help
137536
Review status: Help
criteria provided, multiple submitters, no conflicts2 stars out of maximum of 4 stars

Interpretation Help

Clinical significance:
Benign/Likely benign
Last evaluated:
Jul 20, 2015
Number of submission(s):
2
See supporting ClinVar records

Allele(s) Help

NM_012208.3(HARS2):c.7C>G (p.Leu3Val)

Allele ID:
141239
Variant type:
single nucleotide variant
Cytogenetic location:
5q31.3
Genomic location:
  • Chr5: 140691655 (on Assembly GRCh38)
  • Chr5: 140071240 (on Assembly GRCh37)
Protein change:
L3V
HGVS:
  • NG_021415.1:g.5223C>G
  • NM_001278732.1:c.-304C>G
  • NM_012208.3:c.7C>G
  • NC_000005.10:g.140691655C>G (GRCh38)
  • NP_036340.1:p.Leu3Val
  • NC_000005.9:g.140071240C>G (GRCh37)
  • NM_012208.2:c.7C>G
Links:
dbSNP: 186043734
NCBI 1000 Genomes Browser:
rs186043734
Molecular consequence:
  • NM_001278732.1:c.-304C>G: 5 prime UTR variant SO:0001623
  • NM_012208.3:c.7C>G: missense variant SO:0001583
Allele frequency:
GMAF 0.00120 (G)

Variant frequency in dbGaP Help

NM_012208.3(HARS2):c.7C>G (p.Leu3Val)

GRCh37 Chr5:140071240
Called variantsPotential variants
Sample count42 of 754396 of 26318

Called variants are samples submitted to dbGaP that have the variant allele. Potential variants are SRA runs that display the allele in at least 30% of the reads covering the position, and have 10 or more passing reads covering the position.

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Assertion and evidence details

Germline

Clinical significance
(Last evaluated)
Review status
(Assertion method)
Collection methodCondition(s)
(Mode of inheritance)
OriginCitationsSubmitter - Study nameSubmission accession
Benign
(Apr 21, 2014)
criteria provided, single submitter
(GeneDx Variant Classification (06012015))
clinical testinggermline
    GeneDxSCV000168797.5
    Likely benign
    (Jul 20, 2015)
    criteria provided, single submitter
    (LMM Criteria)
    clinical testinggermline
      Laboratory for Molecular Medicine,Partners HealthCare Personalized MedicineSCV000270263.1
      SubmitterFamiliesIndividualsAllele originEthnicityGeographic originCitations and DatabasesDescription
      Total for all submitters33germlinenot providednot provided
      GeneDxnot providednot providedgermlinenot providednot providednot providedThis variant is considered lik…Full description
      Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine33germlinenot providednot providednot providedp.Leu3Val in exon 1 of HARS2: …Full description
      SubmitterAllele originIndividualsPhenotypes (Affected status)EthnicityGeographic originCitationsDescription

      Last Updated: Aug 12, 2016