NM_000053.4(ATP7B):c.3060+16G>T AND Wilson disease

Clinical significance:Benign/Likely benign (Last evaluated: Feb 25, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000029367.2

Allele description [Variation Report for NM_000053.4(ATP7B):c.3060+16G>T]

NM_000053.4(ATP7B):c.3060+16G>T

Gene:
ATP7B:ATPase copper transporting beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q14.3
Genomic location:
Preferred name:
NM_000053.4(ATP7B):c.3060+16G>T
HGVS:
  • NC_000013.11:g.51946268C>A
  • NG_008806.1:g.70227G>T
  • NM_000053.4:c.3060+16G>TMANE SELECT
  • NM_001005918.3:c.2439+16G>T
  • NM_001243182.1:c.2727+16G>T
  • NM_001330578.1:c.2826+16G>T
  • NM_001330579.2:c.2808+16G>T
  • NC_000013.10:g.52520404C>A
  • NM_000053.3:c.3060+16G>T
  • NM_001005918.2:c.2439+16G>T
Links:
dbSNP: rs76163470
NCBI 1000 Genomes Browser:
rs76163470
Molecular consequence:
  • NM_000053.4:c.3060+16G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001005918.3:c.2439+16G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001243182.1:c.2727+16G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330578.1:c.2826+16G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330579.2:c.2808+16G>T - intron variant - [Sequence Ontology: SO:0001627]
Observations:
2

Condition(s)

Name:
Wilson disease (WND)
Synonyms:
Wilson's disease; Hepatolenticular degeneration
Identifiers:
MONDO: MONDO:0010200; MedGen: C0019202; Orphanet: 905; OMIM: 277900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000052014Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
likely benign
(Aug 18, 2011)
germlinecuration, clinical testing

Citation Link,

SCV000602600ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Benign
(Feb 25, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedcuration
not providedgermlineunknown2not providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052014.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
2not providednot providednot providednot providedclinical testingnot provided
3not providednot providednot providednot providedclinical testingnot provided

Description

Converted during submission to Likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providedBloodassert pathogenicitynot providednot providednot providednot provided
2germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 2
3germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 3

Co-occurrences

#ZygosityAllelesNumber of Observations
2SingleHeterozygoteATP7B:c.3903+6C>T, ATP7B:c.2855G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C1
3SingleHeterozygoteATP7B:c.2866-13G>C, ATP7B:c.3903+6C>T, ATP7B:c.2855G>A, ATP7B:c.2495A>G, ATP7B:c.3419T>C1

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000602600.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2021

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