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NM_000487.6(ARSA):c.854+3A>G AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 27, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000427149.1

Allele description [Variation Report for NM_000487.6(ARSA):c.854+3A>G]

NM_000487.6(ARSA):c.854+3A>G

Gene:
ARSA:arylsulfatase A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_000487.6(ARSA):c.854+3A>G
HGVS:
  • NC_000022.11:g.50626588T>C
  • NG_009260.2:g.6592A>G
  • NM_000487.6:c.854+3A>GMANE SELECT
  • NM_001085425.3:c.854+3A>G
  • NM_001085426.3:c.854+3A>G
  • NM_001085427.3:c.854+3A>G
  • NM_001085428.3:c.596+3A>G
  • NM_001362782.2:c.596+3A>G
  • NC_000022.10:g.51065016T>C
  • NM_000487.5:c.854+3A>G
Links:
dbSNP: rs1057524566
NCBI 1000 Genomes Browser:
rs1057524566
Molecular consequence:
  • NM_000487.6:c.854+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085425.3:c.854+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085426.3:c.854+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085427.3:c.854+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085428.3:c.596+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362782.2:c.596+3A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000535920GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Dec 27, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000535920.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.854+3 A>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.854+3 A>G variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.854+3 A>G nucleotide substitution occurs at a position that is not conserved. Several in-silico splice prediction models predict that c.854+3 A>G destroys the splice donor for intron 4 and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Apr 23, 2022