NM_002047.4(GARS1):c.51G>A (p.Leu17=) AND not specified

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jul 11, 2019
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000517477.6

Allele description [Variation Report for NM_002047.4(GARS1):c.51G>A (p.Leu17=)]

NM_002047.4(GARS1):c.51G>A (p.Leu17=)

Gene:

GARS1:glycyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p14.3

Genomic location:

Preferred name:

NM_002047.4(GARS1):c.51G>A (p.Leu17=)

HGVS:

NC_000007.14:g.30594972G>A
NG_007942.1:g.5408G>A
NM_001316772.1:c.-112G>A
NM_002047.4:c.51G>AMANE SELECT
NP_002038.2:p.Leu17=
LRG_243t1:c.51G>A
LRG_243:g.5408G>A
NC_000007.13:g.30634588G>A
NM_002047.2:c.51G>A
p.Leu17Leu

Links:

dbSNP: rs202117737

NCBI 1000 Genomes Browser:

rs202117737

Molecular consequence:

NM_001316772.1:c.-112G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_002047.4:c.51G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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ATPase copper transporting alpha, partial [Pteropus caniceps]
ATPase copper transporting alpha, partial [Pteropus caniceps]
gi|1825635400|gb|QIQ68748.1|

Protein
Homo sapiens component of oligomeric golgi complex 6 (COG6), RefSeqGene on chrom...
Homo sapiens component of oligomeric golgi complex 6 (COG6), RefSeqGene on chromosome 13
gi|330864701|ref|NG_028352.1|

Nucleotide
Homo sapiens cDNA FLJ32797 fis, clone TESTI2002467
Homo sapiens cDNA FLJ32797 fis, clone TESTI2002467
gi|16553027|dbj|AK057359.1|

Nucleotide
fat-2 Delta(12) fatty acid desaturase fat-2;Fatty acid desaturase [Caenorhabditi...
fat-2 Delta(12) fatty acid desaturase fat-2;Fatty acid desaturase [Caenorhabditis elegans]
Gene ID:178293

Gene
hsp-17 SHSP domain-containing protein [Caenorhabditis elegans]
hsp-17 SHSP domain-containing protein [Caenorhabditis elegans]
Gene ID:186113

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000613382	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Feb 15, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002755203	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jul 11, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000613382

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Feb 15, 2017)

germline

clinical testing

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

SCV002755203

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jul 11, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Athena Diagnostics, SCV000613382.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV002755203.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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