NM_000487.6(ARSA):c.979+8C>T AND Metachromatic leukodystrophy

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Nov 6, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001329926.2

Allele description [Variation Report for NM_000487.6(ARSA):c.979+8C>T]

NM_000487.6(ARSA):c.979+8C>T

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.979+8C>T
HGVS:
  • NC_000022.11:g.50626146G>A
  • NG_009260.2:g.7034C>T
  • NM_000487.6:c.979+8C>TMANE SELECT
  • NM_001085425.3:c.979+8C>T
  • NM_001085426.3:c.979+8C>T
  • NM_001085427.3:c.979+8C>T
  • NM_001085428.3:c.721+8C>T
  • NM_001362782.2:c.721+8C>T
  • NC_000022.10:g.51064574G>A
  • NM_000487.5:c.979+8C>T
Molecular consequence:
  • NM_000487.6:c.979+8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085425.3:c.979+8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085426.3:c.979+8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085427.3:c.979+8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001085428.3:c.721+8C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362782.2:c.721+8C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Metachromatic leukodystrophy (MLD)
Synonyms:
Metachromatic leukoencephalopathy; Sulfatide lipidosis; Cerebral sclerosis diffuse metachromatic form; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0018868; MedGen: C0023522; Orphanet: 512; OMIM: 250100

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001521491Baylor Geneticscriteria provided, single submitter
Uncertain significance
(Jan 17, 2020)
unknownclinical testing

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

SCV001609859Invitaecriteria provided, single submitter
Likely benign
(Nov 6, 2020)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Baylor Genetics, SCV001521491.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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

From Invitae, SCV001609859.1

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

Last Updated: Oct 7, 2021

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