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NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
13 (Most recent: Sep 23, 2021)
Last evaluated:
Jul 14, 2021
Accession:
VCV000021184.9
Variation ID:
21184
Description:
single nucleotide variant
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NM_000487.6(ARSA):c.1178C>G (p.Thr393Ser)

Allele ID
34036
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.33
Genomic location
22: 50625611 (GRCh38) GRCh38 UCSC
22: 51064039 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.51064039G>C
NC_000022.11:g.50625611G>C
NM_000487.6:c.1178C>G MANE Select NP_000478.3:p.Thr393Ser missense
... more HGVS
Protein change
T393S, T307S
Other names
-
Canonical SPDI
NC_000022.11:50625610:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.40555 (C)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.48408
The Genome Aggregation Database (gnomAD) 0.49744
1000 Genomes Project 0.40555
Trans-Omics for Precision Medicine (TOPMed) 0.46659
The Genome Aggregation Database (gnomAD), exomes 0.47985
Exome Aggregation Consortium (ExAC) 0.48431
Links
ClinGen: CA146668
dbSNP: rs743616
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 6 criteria provided, multiple submitters, no conflicts Jul 14, 2021 RCV000020311.7
Benign 5 criteria provided, multiple submitters, no conflicts Mar 16, 2015 RCV000078937.8
Benign 2 criteria provided, single submitter Mar 3, 2015 RCV000675747.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ARSA - - GRCh38
GRCh37
582 718

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 16, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110798.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001888198.1
Submitted: (Sep 17, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 31694723, 29961769, 11941485, 1670590, 20220177)
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: unknown
Mendelics
Accession: SCV001141460.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Invitae
Accession: SCV001728099.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 14, 2021)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001775284.1
Submitted: (Aug 09, 2021)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000304455.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Mar 06, 2018)
criteria provided, single submitter
Method: clinical testing
Metachromatic leukodystrophy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000439431.3
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)
Benign
(Feb 06, 2014)
no assertion criteria provided
Method: literature only
Metachromatic leukodystrophy
Allele origin: germline
GeneReviews
Accession: SCV000040686.2
Submitted: (Jun 22, 2017)
Evidence details
Other databases
https://www.ncbi.nlm.nih.gov/boo…
Comment:
Pseudodeficiency.
Benign
(Jun 07, 2017)
no assertion criteria provided
Method: curation
Metachromatic leukodystrophy
Allele origin: germline
SingHealth Duke-NUS Institute of Precision Medicine
Accession: SCV000853181.1
Submitted: (Apr 09, 2018)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001932021.1
Submitted: (Sep 23, 2021)
Evidence details
Uncertain significance
(Oct 22, 2015)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801465.1
Submitted: (May 23, 2018)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742599.3
Submitted: (Sep 02, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001923929.1
Submitted: (Sep 23, 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
Arylsulfatase A Deficiency Gomez-Ospina N - 2020 PMID: 20301309
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ARSA - - - -
https://www.ncbi.nlm.nih.gov/books/NBK1130/ - - - -

Text-mined citations for rs743616...

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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 Sep 26, 2021