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A variant with different variant types reported in different submissions #4

Open zshuyinggg opened 1 year ago

zshuyinggg commented 1 year ago 

<ClinVarSet ID="92208415">
  <RecordStatus>current</RecordStatus>
  <Title>NM_138694.4(PKHD1):c.8246_8247inv (p.Trp2749Ser) AND not provided</Title>
  <ReferenceClinVarAssertion ID="201743" DateLastUpdated="2022-04-23" DateCreated="2014-01-17">
    <ClinVarAccession Acc="RCV000082578" DateUpdated="2022-04-23" DateCreated="2014-01-17" Version="6" Type="RCV"/>
    <RecordStatus>current</RecordStatus>
    <ClinicalSignificance DateLastEvaluated="2013-03-26">
      <ReviewStatus>criteria provided, single submitter</ReviewStatus>
      <Description>Uncertain significance</Description>
    </ClinicalSignificance>
    <Assertion Type="variation to disease"/>
    <ObservedIn>
      <Sample>
        <Origin>germline</Origin>
        <Species TaxonomyId="9606">human</Species>
        <AffectedStatus>unknown</AffectedStatus>
      </Sample>
      <Method>
        <MethodType>clinical testing</MethodType>
      </Method>
      <ObservedData ID="95897660">
        <Attribute integerValue="1" Type="VariantAlleles"/>
      </ObservedData>
    </ObservedIn>
    <MeasureSet Type="Variant" ID="96428" Acc="VCV000096428" Version="3">
!!!!!!!!!!!!!!!!!!!!!!!!<Measure Type="Inversion" ID="102322">
        <Name>
          <ElementValue Type="Preferred">NM_138694.4(PKHD1):c.8246_8247inv (p.Trp2749Ser)</ElementValue>
        </Name>
        <CanonicalSPDI>NC_000006.12:51830915:CC:GG</CanonicalSPDI>
        <AttributeSet>
          <Attribute Accession="NM_138694" Version="4" Change="c.8246_8247inv" Type="HGVS, coding, RefSeq" MANESelect="true">NM_138694.4:c.8246_8247inv</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NM_170724" Version="3" Change="c.8246_8247inv" Type="HGVS, coding, RefSeq">NM_170724.3:c.8246_8247inv</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NG_008753" Version="1" Change="g.261709_261710inv" Type="HGVS, genomic, RefSeqGene">NG_008753.1:g.261709_261710inv</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NC_000006" Version="12" Change="g.51830916_51830917inv" Type="HGVS, genomic, top level" integerValue="38">NC_000006.12:g.51830916_51830917inv</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NC_000006" Version="11" Change="g.51695714_51695715inv" Type="HGVS, genomic, top level, previous" integerValue="37">NC_000006.11:g.51695714_51695715inv</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NM_138694" Version="3" Change="c.8246_8247delGGinsCC" Type="HGVS, previous">NM_138694.3:c.8246_8247delGGinsCC</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NP_619639" Version="3" Change="p.Trp2749Ser" Type="HGVS, protein, RefSeq">NP_619639.3:p.Trp2749Ser</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NP_733842" Version="2" Change="p.Trp2749Ser" Type="HGVS, protein, RefSeq">NP_733842.2:p.Trp2749Ser</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="Location">NM_138694.3:exon 52</Attribute>
          <XRef ID="CX100430" DB="HGMD"/>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="MolecularConsequence">missense variant</Attribute>
          <XRef ID="SO:0001583" DB="Sequence Ontology"/>
          <XRef ID="NM_138694.4:c.8246_8247inv" DB="RefSeq"/>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="MolecularConsequence">missense variant</Attribute>
          <XRef ID="SO:0001583" DB="Sequence Ontology"/>
          <XRef ID="NM_170724.3:c.8246_8247inv" DB="RefSeq"/>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="ProteinChange1LetterCode">W2749S</Attribute>
        </AttributeSet>
        <CytogeneticLocation>6p12.2</CytogeneticLocation>
        <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="6" Accession="NC_000006.12" start="51830916" stop="51830917" display_start="51830916" display_stop="51830917" variantLength="2" positionVCF="51830916" referenceAlleleVCF="CC" alternateAlleleVCF="GG"/>
        <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="6" Accession="NC_000006.11" start="51695714" stop="51695715" display_start="51695714" display_stop="51695715" variantLength="2" positionVCF="51695714" referenceAlleleVCF="CC" alternateAlleleVCF="GG"/>
        <MeasureRelationship Type="within single gene">
          <Name>
            <ElementValue Type="Preferred">PKHD1 ciliary IPT domain containing fibrocystin/polyductin</ElementValue>
          </Name>
          <Symbol>
            <ElementValue Type="Preferred">PKHD1</ElementValue>
          </Symbol>
          <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="6" Accession="NC_000006.12" start="51615299" stop="52087615" display_start="51615299" display_stop="52087615" Strand="-"/>
          <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="6" Accession="NC_000006.11" start="51480144" stop="51952422" display_start="51480144" display_stop="51952422" variantLength="472279" Strand="-"/>
          <XRef ID="5314" DB="Gene"/>
          <XRef Type="MIM" ID="606702" DB="OMIM"/>
          <XRef ID="HGNC:9016" DB="HGNC"/>
        </MeasureRelationship>
      </Measure>
      <Name>
        <ElementValue Type="Preferred">NM_138694.4(PKHD1):c.8246_8247inv (p.Trp2749Ser)</ElementValue>
      </Name>
      <XRef ID="CA224096" DB="ClinGen"/>
    </MeasureSet>
    <TraitSet Type="Disease" ID="9460">
      <Trait ID="17556" Type="Disease">
        <Name>
          <ElementValue Type="Preferred">not provided</ElementValue>
          <XRef ID="13DG0619" DB="Developmental Genetics Unit,King Faisal Specialist Hospital &amp; Research Centre"/>
        </Name>
        <Name>
          <ElementValue Type="Alternate">none provided</ElementValue>
        </Name>
        <AttributeSet>
          <Attribute Type="public definition">The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified.</Attribute>
        </AttributeSet>
        <XRef ID="CN517202" DB="MedGen"/>
      </Trait>
    </TraitSet>
  </ReferenceClinVarAssertion>
  <ClinVarAssertion ID="196731" SubmissionName="SUB4534263">
    <ClinVarSubmissionID localKey="8737_000000" localKeyIsSubmitted="1" submittedAssembly="GRCh37" submitter="Eurofins NTD LLC (GA)" submitterDate="2018-09-19"/>
    <ClinVarAccession Acc="SCV000114620" DateCreated="2014-01-17" DateUpdated="2015-06-29" Version="8" Type="SCV" OrgID="500060" OrganizationCategory="laboratory" OrgType="primary"/>
    <RecordStatus>current</RecordStatus>
    <ClinicalSignificance DateLastEvaluated="2013-03-26">
      <ReviewStatus>criteria provided, single submitter</ReviewStatus>
      <Description>Uncertain significance</Description>
    </ClinicalSignificance>
    <Assertion Type="variation to disease"/>
    <ExternalID DB="EGL Genetic Diagnostics" ID="8737"/>
    <AttributeSet>
      <Attribute Type="AssertionMethod">EGL Classification Definitions 2015</Attribute>
      <Citation>
        <URL>https://submit.ncbi.nlm.nih.gov/ft/byid/ahdynye1/egl_classification_definitions_2015.pdf</URL>
      </Citation>
    </AttributeSet>
    <ObservedIn>
      <Sample>
        <Origin>germline</Origin>
        <Species TaxonomyId="9606">human</Species>
        <AffectedStatus>unknown</AffectedStatus>
        <Gender>mixed</Gender>
      </Sample>
      <Method>
        <MethodType>clinical testing</MethodType>
      </Method>
      <ObservedData>
        <Attribute Type="VariantAlleles" integerValue="1"/>
      </ObservedData>
      <ObservedData>
        <Attribute Type="SingleHeterozygote" integerValue="1"/>
      </ObservedData>
    </ObservedIn>
    <MeasureSet Type="Variant">
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<Measure Type="Indel">
        <AttributeSet>
          <Attribute Type="Location">NM_138694.3:Ex52</Attribute>
        </AttributeSet>
        <SequenceLocation Assembly="GRCh37" Chr="6" alternateAllele="GG" referenceAllele="CC" start="51695714" stop="51695715" variantLength="2"/>
        <MeasureRelationship Type="variant in gene">
          <Symbol>
            <ElementValue Type="Preferred">PKHD1</ElementValue>
          </Symbol>
        </MeasureRelationship>
        <XRef DB="HGMD" ID="CX100430"/>
      </Measure>
    </MeasureSet>
    <TraitSet Type="Disease">
      <Trait Type="Disease">
        <Name>
          <ElementValue Type="Preferred">not provided</ElementValue>
        </Name>
      </Trait>
    </TraitSet>
    <Citation>
      <URL>http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PKHD1</URL>
    </Citation>
  </ClinVarAssertion>
</ClinVarSet>