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Variant type 'indel' leads to single amino acid change #5

Open zshuyinggg opened 1 year ago

zshuyinggg commented 1 year ago 

<ClinVarSet ID="92299651">
  <RecordStatus>current</RecordStatus>
  <Title>NM_003036.4(SKI):c.499_500delinsGG (p.Leu167Gly) AND not provided</Title>
  <ReferenceClinVarAssertion ID="475644" DateLastUpdated="2022-04-23" DateCreated="2015-10-11">
    <ClinVarAccession Acc="RCV000200337" DateUpdated="2022-04-23" DateCreated="2015-10-11" Version="3" Type="RCV"/>
    <RecordStatus>current</RecordStatus>
    <ClinicalSignificance DateLastEvaluated="2020-04-17">
      <ReviewStatus>criteria provided, single submitter</ReviewStatus>
      <Description>Likely pathogenic</Description>
    </ClinicalSignificance>
    <Assertion Type="variation to disease"/>
    <ObservedIn>
      <Sample>
        <Origin>germline</Origin>
        <Species TaxonomyId="9606">human</Species>
        <AffectedStatus>yes</AffectedStatus>
      </Sample>
      <Method>
        <MethodType>clinical testing</MethodType>
      </Method>
      <ObservedData ID="97202348">
        <Attribute Type="Description">not provided</Attribute>
      </ObservedData>
    </ObservedIn>
    <MeasureSet Type="Variant" ID="213703" Acc="VCV000213703" Version="3">
      <Measure Type="Indel" ID="209450">
        <Name>
          <ElementValue Type="Preferred">NM_003036.4(SKI):c.499_500delinsGG (p.Leu167Gly)</ElementValue>
        </Name>
        <Name>
          <ElementValue Type="Alternate">p.L167G:CTG&gt;GGG</ElementValue>
        </Name>
        <CanonicalSPDI>NC_000001.11:2229264:CT:GG</CanonicalSPDI>
        <AttributeSet>
          <Attribute Accession="NM_003036" Version="3" Change="c.499_500delCTinsGG" Type="HGVS, coding">NM_003036.3:c.499_500delCTinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NM_003036" Version="4" Change="c.499_500delinsGG" Type="HGVS, coding, RefSeq" MANESelect="true">NM_003036.4:c.499_500delinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NG_013084" Version="1" Change="g.5571_5572delinsGG" Type="HGVS, genomic, RefSeqGene">NG_013084.1:g.5571_5572delinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NC_000001" Version="11" Change="g.2229265_2229266delinsGG" Type="HGVS, genomic, top level" integerValue="38">NC_000001.11:g.2229265_2229266delinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NC_000001" Version="10" Change="g.2160704_2160705delinsGG" Type="HGVS, genomic, top level, previous" integerValue="37">NC_000001.10:g.2160704_2160705delinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NM_003036" Version="3" Change="c.499_500delinsGG" Type="HGVS, previous">NM_003036.3:c.499_500delinsGG</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Accession="NP_003027" Version="1" Change="p.Leu167Gly" Type="HGVS, protein, RefSeq">NP_003027.1:p.Leu167Gly</Attribute>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="MolecularConsequence">missense variant</Attribute>
          <XRef ID="SO:0001583" DB="Sequence Ontology"/>
          <XRef ID="NM_003036.4:c.499_500delinsGG" DB="RefSeq"/>
        </AttributeSet>
        <AttributeSet>
          <Attribute Type="ProteinChange1LetterCode">L167G</Attribute>
        </AttributeSet>
        <CytogeneticLocation>1p36.33</CytogeneticLocation>
        <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="1" Accession="NC_000001.11" start="2229265" stop="2229266" display_start="2229265" display_stop="2229266" variantLength="2" positionVCF="2229265" referenceAlleleVCF="CT" alternateAlleleVCF="GG"/>
        <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="1" Accession="NC_000001.10" start="2160704" stop="2160705" display_start="2160704" display_stop="2160705" variantLength="2" positionVCF="2160704" referenceAlleleVCF="CT" alternateAlleleVCF="GG"/>
        <MeasureRelationship Type="within single gene">
          <Name>
            <ElementValue Type="Preferred">SKI proto-oncogene</ElementValue>
          </Name>
          <Symbol>
            <ElementValue Type="Preferred">SKI</ElementValue>
          </Symbol>
          <AttributeSet>
            <Attribute dateValue="2012-01-06" Type="Haploinsufficiency">No evidence available</Attribute>
            <Citation>
              <URL>https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=SKI</URL>
            </Citation>
          </AttributeSet>
          <AttributeSet>
            <Attribute dateValue="2012-01-06" Type="Triplosensitivity">No evidence available</Attribute>
            <Citation>
              <URL>https://www.ncbi.nlm.nih.gov/projects/dbvar/ISCA/isca_gene.cgi?sym=SKI</URL>
            </Citation>
          </AttributeSet>
          <SequenceLocation Assembly="GRCh38" AssemblyAccessionVersion="GCF_000001405.38" AssemblyStatus="current" Chr="1" Accession="NC_000001.11" start="2228319" stop="2310213" display_start="2228319" display_stop="2310213" Strand="+"/>
          <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25" AssemblyStatus="previous" Chr="1" Accession="NC_000001.10" start="2160133" stop="2241651" display_start="2160133" display_stop="2241651" variantLength="81519" Strand="+"/>
          <XRef ID="6497" DB="Gene"/>
          <XRef Type="MIM" ID="164780" DB="OMIM"/>
          <XRef ID="HGNC:10896" DB="HGNC"/>
        </MeasureRelationship>
        <XRef Type="rs" ID="863223724" DB="dbSNP"/>
      </Measure>
      <Name>
        <ElementValue Type="Preferred">NM_003036.4(SKI):c.499_500delinsGG (p.Leu167Gly)</ElementValue>
      </Name>
      <AttributeSet>
        <Attribute Type="SubmitterVariantId">GDX:57661</Attribute>
      </AttributeSet>
      <XRef ID="CA324894" 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="465778">
    <ClinVarSubmissionID localKey="GDXSV:178678" localKeyIsSubmitted="1" submitter="GeneDx" submitterDate="2021-09-30"/>
    <ClinVarAccession Acc="SCV000250689" DateCreated="2015-10-11" DateUpdated="2021-10-02" Version="12" Type="SCV" OrgID="26957" OrganizationCategory="laboratory" OrgType="primary"/>
    <RecordStatus>current</RecordStatus>
    <ClinicalSignificance DateLastEvaluated="2020-04-17">
      <ReviewStatus>criteria provided, single submitter</ReviewStatus>
      <Description>Likely pathogenic</Description>
      <Comment>Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge</Comment>
    </ClinicalSignificance>
    <Assertion Type="variation to disease"/>
    <AttributeSet>
      <Attribute Type="AssertionMethod">GeneDX Variant Classification (06012015)</Attribute>
      <Citation>
        <URL>https://submit.ncbi.nlm.nih.gov/ft/byid/fc81e176/genedx_variant_classification_process_june_2021.pdf</URL>
      </Citation>
    </AttributeSet>
    <ObservedIn>
      <Sample>
        <Origin>germline</Origin>
        <Species TaxonomyId="9606">human</Species>
        <AffectedStatus>yes</AffectedStatus>
      </Sample>
      <Method>
        <MethodType>clinical testing</MethodType>
      </Method>
      <ObservedData>
        <Attribute Type="Description">not provided</Attribute>
      </ObservedData>
    </ObservedIn>
    <MeasureSet Type="Variant">
      <Measure Type="Indel">
        <AttributeSet>
          <Attribute Type="HGVS">NM_003036.3:c.499_500delinsGG</Attribute>
        </AttributeSet>
        <MeasureRelationship Type="variant in gene">
          <Symbol>
            <ElementValue Type="Preferred">SKI</ElementValue>
          </Symbol>
        </MeasureRelationship>
      </Measure>
      <AttributeSet>
        <Attribute Type="SubmitterVariantId">GDX:57661</Attribute>
      </AttributeSet>
    </MeasureSet>
    <TraitSet Type="Disease">
      <Trait Type="Disease">
        <Name>
          <ElementValue Type="Preferred">Not Provided</ElementValue>
        </Name>
      </Trait>
    </TraitSet>
  </ClinVarAssertion>
</ClinVarSet>