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NM_000156.6(GAMT):c.279C>T (p.Asp93=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000137434.7
Variation ID:
137434
Description:
single nucleotide variant
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NM_000156.6(GAMT):c.279C>T (p.Asp93=)

Allele ID
141137
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1399841 (GRCh38) GRCh38 UCSC
19: 1399840 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.1399841G>A
NC_000019.9:g.1399840G>A
NM_000156.6:c.279C>T MANE Select NP_000147.1:p.Asp93= synonymous
... more HGVS
Protein change
-
Other names
p.D93D:GAC>GAT
Canonical SPDI
NC_000019.10:1399840:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00068
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Exome Aggregation Consortium (ExAC) 0.00118
The Genome Aggregation Database (gnomAD), exomes 0.00058
The Genome Aggregation Database (gnomAD) 0.00057
1000 Genomes Project 0.00060
Links
ClinGen: CA291015
dbSNP: rs144630886
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 26, 2016 RCV000125190.4
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000655373.4
Likely benign 1 criteria provided, single submitter Dec 29, 2016 RCV000720558.1
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001127002.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAMT - - GRCh38
GRCh37
330 374

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(May 19, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000168631.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Jan 26, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000338385.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of guanidinoacetate methyltransferase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001286264.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Dec 29, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000851437.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Cerebral creatine deficiency syndrome
Allele origin: germline
Invitae
Accession: SCV000777303.4
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAMT - - - -

Text-mined citations for rs144630886...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021