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NM_020320.5(RARS2):c.78A>C (p.Thr26=) AND not provided

Germline classification:
Conflicting classifications of pathogenicity (5 submissions)
Last evaluated:
Dec 1, 2024
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000676836.27

Allele description [Variation Report for NM_020320.5(RARS2):c.78A>C (p.Thr26=)]

NM_020320.5(RARS2):c.78A>C (p.Thr26=)

Gene:
RARS2:arginyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q15
Genomic location:
Preferred name:
NM_020320.5(RARS2):c.78A>C (p.Thr26=)
HGVS:
  • NC_000006.12:g.87569549T>G
  • NG_008601.1:g.25469A>C
  • NM_001318785.2:c.-392A>C
  • NM_001350505.2:c.78A>C
  • NM_001350506.2:c.-448A>C
  • NM_001350507.2:c.-448A>C
  • NM_001350508.2:c.-610A>C
  • NM_001350509.2:c.-359-5317A>C
  • NM_001350510.2:c.-448A>C
  • NM_001350511.2:c.-567A>C
  • NM_020320.5:c.78A>CMANE SELECT
  • NP_001337434.1:p.Thr26=
  • NP_064716.2:p.Thr26=
  • NC_000006.11:g.88279267T>G
  • NM_020320.3:c.78A>C
  • NR_134857.2:n.108A>C
  • NR_146738.2:n.329A>C
  • NR_146739.2:n.329A>C
  • NR_146740.2:n.329A>C
  • NR_146742.2:n.329A>C
  • NR_146743.2:n.329A>C
  • NR_146744.2:n.329A>C
  • NR_146745.2:n.329A>C
  • NR_146746.2:n.547A>C
  • NR_146747.2:n.108A>C
  • NR_146748.2:n.329A>C
  • NR_146749.2:n.329A>C
  • NR_146750.2:n.329A>C
  • NR_146751.2:n.329A>C
  • NR_146752.2:n.329A>C
  • NR_146753.2:n.329A>C
  • NR_146754.2:n.329A>C
  • NR_146755.2:n.329A>C
  • NR_146756.2:n.108A>C
  • NR_146758.2:n.329A>C
  • NR_146759.2:n.329A>C
Links:
dbSNP: rs138360045
NCBI 1000 Genomes Browser:
rs138360045
Molecular consequence:
  • NM_001318785.2:c.-392A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350506.2:c.-448A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350507.2:c.-448A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350508.2:c.-610A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350510.2:c.-448A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350511.2:c.-567A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001350509.2:c.-359-5317A>C - intron variant - [Sequence Ontology: SO:0001627]
  • NR_134857.2:n.108A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146738.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146739.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146740.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146742.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146743.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146744.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146745.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146746.2:n.547A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146747.2:n.108A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146748.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146749.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146750.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146751.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146752.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146753.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146754.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146755.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146756.2:n.108A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146758.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146759.2:n.329A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001350505.2:c.78A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_020320.5:c.78A>C - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000227491Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Uncertain significance
(Feb 20, 2015) 		germlineclinical testing

Citation Link,

SCV000802646Mayo Clinic Laboratories, Mayo Clinic
no assertion criteria provided
Likely benign
(Mar 9, 2016) 		unknownclinical testing

SCV001005055Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Oct 17, 2024) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001836604GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely benign
(May 22, 2021) 		germlineclinical testing

Citation Link,

SCV005892562CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Likely benign
(Dec 1, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Eurofins Ntd Llc (ga), SCV000227491.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000802646.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001005055.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001836604.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV005892562.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

RARS2: BP4, BP7

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 22, 2025