Version: 3.24 (unreleased)

ClinVar Preview

Overview

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation.

Publication

Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Karen Karapetyan, Kenneth Katz, Chunlei Liu, Zenith Maddipatla, Adriana Malheiro, Kurt McDaniel, Michael Ovetsky, George Riley, George Zhou, J Bradley Holmes, Brandi L Kattman, Donna R Maglott, ClinVar: improving access to variant interpretations and supporting evidence, Nucleic Acids Research, 46, Issue D1, 4 January 2018, Pages D1062–D1067, https://doi.org/10.1093/nar/gkx1153

ClinVar Preview relates to the new ClinVar XML format introduced in 2024. Following sections describe the parsing and subsequent json format provided by Illumina Connected Annotations.

Parsing

ClinVar recommends using the VCV XML file because it contains comprehensive information.

Parsing is simplified by using the XSD file generation. Command for generating XSD file

xsd ClinVar_VCV.xsd /n:VariationArchive /c

Overall XML to JSON mapping

key	type	description	XML path
`variantType`	string	sequence ontology	`VariationArchive.VariationType`
`accession`	string	VCV Id from ClinVar	`VariationArchive.Accession`
`version`	string	VCV Id version	`VariationArchive.Version`
`recordType`	string	`classified`	`VariationArchive.RecordType`
`dateLastUpdated`	date time	date VCV was last updated	`VariationArchive.DateLastUpdated`
`chromosome`	string	chromosome (large variants only)	`VariationArchive.ClassifiedRecord.SimpleAllele.Location.SequenceLocation.Chr`
`begin`	number	start position of the variant (large variants only)	`VariationArchive.ClassifiedRecord.SimpleAllele.Location.SequenceLocation.positionVCF`
`end`	number	end position of the variant (large variants only)	`VariationArchive.ClassifiedRecord.SimpleAllele.Location.SequenceLocation.displayStop` or calculated
`refAllele`	string	reference alleles (small variants only)	`VariationArchive.ClassifiedRecord.SimpleAllele.Location.SequenceLocation.referenceAlleleVCF`
`altAllele`	string	alternate alleles (small variants only)	`VariationArchive.ClassifiedRecord.SimpleAllele.Location.SequenceLocation.alternateAlleleVCF`
`rcvs`	list	list of RCV objects	`VariationArchive.ClassifiedRecord.RCVList`
`classifications`	list	list of classification objects	`VariationArchive.ClassifiedRecord.Classifications`
`clinicalAssertions`	list	list of clinicalAssertion objects	`VariationArchive.ClassifiedRecord.ClinicalAssertionList`

Variation fields

XML

<VariationArchive
    VariationID="1381081"
    VariationName="NM_003000.3(SDHB):c.19_41dup (p.Pro14_Ala15insSerProTer)"
    VariationType="Indel"
    Accession="VCV001381081"
    Version="3"
    RecordType="classified"
    DateLastUpdated="2024-01-26"
    NumberOfSubmissions="1"
    NumberOfSubmitters="1"
    DateCreated="2022-03-28"
    MostRecentSubmission="2023-02-07"
>
...

JSON

{
  "variantType": "delins",
  "accession": "VCV001381081",
  "version": "3",
  "recordType": "classified",
  "dateLastUpdated": "2024-01-26",
  ...
}

Location fields

<SimpleAllele
    AlleleID="196495"
    VariationID="1381081"
    >
    <Location>
        <CytogeneticLocation>1p36.13</CytogeneticLocation>
        <SequenceLocation
            Accession="NC_000001.11"
            Chr="1"
            Assembly="GRCh38"
            positionVCF="17053978"
            referenceAlleleVCF="C"
            alternateAlleleVCF="CGGCAACCGGCGCCTCAAGGAGAG"
            display_start="17053978"
            display_stop="17053979"
            AssemblyAccessionVersion="GCF_000001405.38"
            forDisplay="true"
            AssemblyStatus="current"
            start="17053978"
            stop="17053979"
            variantLength="23"
        />
        <SequenceLocation Assembly="GRCh37" AssemblyAccessionVersion="GCF_000001405.25"
                          AssemblyStatus="previous" Chr="1" Accession="NC_000001.10" start="17380473"
                          stop="17380474" display_start="17380473" display_stop="17380474"
                          variantLength="23" positionVCF="17380473" referenceAlleleVCF="C"
                          alternateAlleleVCF="CGGCAACCGGCGCCTCAAGGAGAG"/>
    </Location>
    ...
    </SimpleAllele>

JSON Small Variant

note the alleles are trimmed

{
  "altAllele": "GGCAACCGGCGCCTCAAGGAGAG",
  "refAllele": "-",
  ...
}

JSON Large Variant

{
  "chromosome": "17",
  "begin": 150732,
  "end": 14764202,
  ...
}

RCVs

RCV Object from XML path VariationArchive.ClassifiedRecord.RCVList

key	type	description	XML sub-path
`accession`	string	VCV Id from ClinVar	`RCVList.RCVAccession.Accession`
`version`	string	VCV Id version	`RCVList.RCVAccession.Accession`
`classifications`	list	list of classification objects	`RCVList.RCVAccession.RCVClassifications`
`classifiedConditions`	list	list of classified conditions	`RCVList.RCVAccession.ClassifiedConditionList`

XML

<RCVList>
    <RCVAccession
        Title="NM_003000.3(SDHB):c.19_41dup (p.Pro14_Ala15insSerProTer) AND multiple conditions"
        Accession="RCV001921860"
        Version="3">
        <ClassifiedConditionList TraitSetID="23696">
            ...
        </ClassifiedConditionList>
        <RCVClassifications>
            ...
        </RCVClassifications>
    </RCVAccession>
</RCVList>
...

JSON

{
  "rcvs": [
    {
      "accession": "RCV001921860",
      "version": "3",
      "classifications": {
        ...
      },
      "classifiedConditions": [
        ...
      ]
    }
  ]
}

Classifications

Classification object from XML path VariationArchive.ClassifiedRecord.RCVList.RCVAccession.RCVClassifications classification can be of following types:

germlineClassification
somaticClinicalImpact
oncogenicityClassification

Germline Classification

Classification object from XML path VariationArchive.ClassifiedRecord.RCVList.RCVAccession.RCVClassifications.GermlineClassification

key	type	description	XML sub-path
`reviewStatus`	string	review status	`GermlineClassification.ReviewStatus`
`descriptions`	list	list of classification objects	`GermlineClassification.Description`
`descriptions[].classification`	string	classification	`GermlineClassification.Description.Value`
`descriptions[].dateLastEvaluated`	date	date last evaluated	`GermlineClassification.Description.DateLastEvaluated`

XML

<RCVClassifications>
    <GermlineClassification>
        <ReviewStatus>criteria provided, single submitter</ReviewStatus>
        <Description DateLastEvaluated="2021-08-04" SubmissionCount="1">Pathogenic</Description>
    </GermlineClassification>
</RCVClassifications>

JSON

{
  "classifications": {
    "germlineClassification": {
      "reviewStatus": "criteria provided, single submitter",
      "descriptions": [
        {
          "dateLastEvaluated": "2021-08-04",
          "classification": "Pathogenic"
        }
      ]
    }
  }
}

Classified Conditions

Classified conditions object from XML path VariationArchive.ClassifiedRecord.RCVList.RCVAccession.ClassifiedConditionList

key	type	description	XML sub-path
`condition`	string	VCV Id from ClinVar	`ClassifiedConditionList.ClassifiedCondition.Value`
`db`	string	list of classification objects	`ClassifiedConditionList.ClassifiedCondition.DB`
`id`	string	classification	`ClassifiedConditionList.ClassifiedCondition.ID`

XML

<ClassifiedConditionList TraitSetID="23696">
    <ClassifiedCondition DB="MedGen" ID="C0238198">Gastrointestinal stromal tumor</ClassifiedCondition>
    <ClassifiedCondition DB="MedGen" ID="C1861848">Paragangliomas 4</ClassifiedCondition>
    <ClassifiedCondition DB="MedGen" ID="C0031511">Pheochromocytoma</ClassifiedCondition>
</ClassifiedConditionList>

JSON

{
  "classifiedConditions": [
    {
      "condition": "Gastrointestinal stromal tumor",
      "db": "MedGen",
      "id": "C0238198"
    },
    {
      "condition": "Paragangliomas 4",
      "db": "MedGen",
      "id": "C1861848"
    },
    {
      "condition": "Pheochromocytoma",
      "db": "MedGen",
      "id": "C0031511"
    }
  ]
}

Classifications

Classification object from XML path VariationArchive.ClassifiedRecord.Classifications classification can be of following types:

germlineClassification
somaticClinicalImpact
oncogenicityClassification

XML

<Classifications>
    <GermlineClassification DateLastEvaluated="2021-08-04" NumberOfSubmissions="1" NumberOfSubmitters="1"
                            DateCreated="2022-03-28" MostRecentSubmission="2023-02-07">
    ...
    </GermlineClassification>
</Classifications>

JSON

"classifications": {
    "germlineClassification": {...}
}

Germline Classification

Classification object from XML path VariationArchive.ClassifiedRecord.Classifications.GermlineClassification

key	type	description	XML sub-path
`classification`	string	classification	`GermlineClassification.Description`
`reviewStatus`	string	review status	`GermlineClassification.ReviewStatus`
`dateLastEvaluated`	date	date last evaluated	`GermlineClassification.DateLastEvaluated`
`mostRecentSubmission`	date	date last evaluated	`GermlineClassification.MostRecentSubmission`
`pubMedIds`	list	list of PubMedIds	`GermlineClassification.Citation.ID.Value`
`conditions`	list	list of conditions	`GermlineClassification.ConditionList`

XML

<Classifications>
    <GermlineClassification DateLastEvaluated="2021-08-04" NumberOfSubmissions="1" NumberOfSubmitters="1"
                            DateCreated="2022-03-28" MostRecentSubmission="2023-02-07">
        <ReviewStatus>criteria provided, single submitter</ReviewStatus>
        <Description>Pathogenic</Description>
        <Citation Type="general">
            <ID Source="PubMed">19454582</ID>
        </Citation>
        <Citation Type="general">
            <ID Source="PubMed">19802898</ID>
        </Citation>
        <ConditionList>
            ...
        </ConditionList>
    </GermlineClassification>
</Classifications>

JSON

{
  "classifications": {
    "germlineClassification": {
      "classification": "Pathogenic",
      "reviewStatus": "criteria provided, single submitter",
      "dateLastEvaluated": "2021-08-04",
      "mostRecentSubmission": "2023-02-07",
      "conditions": [...],
      "pubMedIds": [
        "19454582",
        "19802898"
      ]
    }
  }
}

Conditions

Conditions object from XML path VariationArchive.ClassifiedRecord.Classifications.GermlineClassification.ConditionList

key	type	description	XML sub-path
`type`	string	classification	`ConditionList.TraitSet.Type`
`contributesToAggregateClassification`	True or blank	contributes to aggregate classifcation	`ConditionList.TraitSet.ContributesToAggregateClassification`
`traits`	list	trait objects	`ConditionList.TraitSet.Trait`
`traits[].id`	date	date last evaluated	`ConditionList.TraitSet.Trait`
`traits[].name`	object	trait name object	`ConditionList.TraitSet.Trait`
`traits[].name.value`	string	preferred trait name	`ConditionList.TraitSet.Trait.Name.ElementValue.Type`
`traits[].name.xRefs`	list	list of cross references	`ConditionList.TraitSet.Trait.Name.XRef`
`traits[].name.xRefs[].db`	string	preferred name cross reference database	`ConditionList.TraitSet.Trait.Name.XRef.DB`
`traits[].name.xRefs[].id`	string	preferred name cross reference identifier	`ConditionList.TraitSet.Trait.Name.XRef.ID`

XML

<Classifications>
    <GermlineClassification DateLastEvaluated="2021-08-04" NumberOfSubmissions="1" NumberOfSubmitters="1"
                            DateCreated="2022-03-28" MostRecentSubmission="2023-02-07">
        <ConditionList>
            <TraitSet ID="23696" Type="Disease" ContributesToAggregateClassification="true">
                <Trait ID="3796" Type="Disease">
                    <Name>
                        <ElementValue Type="Preferred">Pheochromocytoma</ElementValue>
                        <XRef ID="Pheochromocytoma/5718" DB="Genetic Alliance"/>
                        <XRef ID="HP:0002666" DB="Human Phenotype Ontology"/>
                        <XRef ID="MONDO:0008233" DB="MONDO"/>
                    </Name>
                    <Name>
                        <ElementValue Type="Alternate">Chromaffinoma</ElementValue>
                    </Name>
                    ...
                </Trait>
            </TraitSet>
        </ConditionList>
    </GermlineClassification>
</Classifications>

JSON

{
  "classifications": {
    "germlineClassification": {
      "classification": "Pathogenic",
      "reviewStatus": "criteria provided, single submitter",
      "dateLastEvaluated": "2021-08-04",
      "mostRecentSubmission": "2023-02-07",
      "conditions": [
        {
          "type": "Disease",
          "contributesToAggregateClassification": true,
          "traits": [
            {
              "id": "3796",
              "name": {
                "xRefs": [
                  {
                    "db": "Genetic Alliance",
                    "id": "Pheochromocytoma/5718"
                  },
                  {
                    "db": "Human Phenotype Ontology",
                    "id": "HP:0002666"
                  },
                  {
                    "db": "MONDO",
                    "id": "MONDO:0008233"
                  }
                ],
                "value": "Pheochromocytoma"
              }
            }
          ]
        }
      ],
      "pubMedIds": [
        "19454582",
        "19802898"
      ]
    }
  }
}

Clinical Assertions

Conditions object from XML path VariationArchive.ClassifiedRecord.ClinicalAssertionList

key	type	description	XML sub-path
`accession`	string	SCV Id from ClinVar	`ClinicalAssertionList.ClinVarAccession.Accession`
`pubMedIds`	list	list of PubMedIds	`ClinicalAssertionList.ClinicalAssertion.AttributeSet.Citation.ID.Value`

XML

<ClinicalAssertionList>
    <ClinicalAssertion ID="4172562" SubmissionDate="2023-01-11" DateLastUpdated="2023-02-07"
                       DateCreated="2022-03-28">
        <ClinVarSubmissionID localKey="12475853|MedGen:C0238198;C1861848;C0031511"
                             submittedAssembly="GRCh37"/>
        <ClinVarAccession
            Accession="SCV002152762"
            DateUpdated="2023-02-07"
            DateCreated="2022-03-28"
            Type="SCV"
            Version="2"
            SubmitterName="Invitae"
            OrgID="500031"
            OrganizationCategory="laboratory"
            OrgAbbreviation="Invitae"
        />
        <RecordStatus>current</RecordStatus>
        <Classification DateLastEvaluated="2021-08-04">
            ...
        </Classification>
        <Assertion>variation to disease</Assertion>
        <AttributeSet>
            <Attribute Type="AssertionMethod">Invitae Variant Classification Sherloc (09022015)</Attribute>
            <Citation>
                <ID Source="PubMed">28492532</ID>
            </Citation>
        </AttributeSet>
        <ObservedInList>
            ...
        </ObservedInList>
        <SimpleAllele>
            ...
        </SimpleAllele>
        <TraitSet Type="Disease">
            ...
        </TraitSet>
        <SubmissionNameList>
            ...
        </SubmissionNameList>
    </ClinicalAssertion>
</ClinicalAssertionList>

JSON

{
"clinicalAssertions": [
    {
      "accession": "SCV002152762",
      "pubMedIds": [
        "28492532"
      ]
    }
  ]
}

Known Issues

Entries with following missing/incorrect information are skipped

Invalid Ref Allele (example VCV000437934)
Invalid Alt Allele (example VCV000006637)
Following variant types are not supported:
1. Variation (example VCV000001101)
2. fusion (example VCV000015269)
3. unknown (example VCV000017564)
4. protein only (example VCV000132152)
5. Complex (example VCV000221337)
6. Translocation (example VCV000267801)
7. no_sequence_alteration (example VCV000010504)
Only records of type classified are included [VCV with type included is skipped (example VCV000431749)]
Records with missing genomic location are skipped (example VCV000000254)

Download URLs

https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarVCVRelease_00-latest.xml.gz

JSON Output

small variants:

{
  "clinvar-preview": [
    {
      "altAllele": "A",
      "refAllele": "G",
      "variantType": "SNV",
      "accession": "VCV000437934",
      "version": "1",
      "recordType": "classified",
      "dateLastUpdated": "2023-08-06",
      "rcvs": [
        {
          "accession": "RCV000505090",
          "version": "1",
          "classifications": {
            "germlineClassification": {
              "reviewStatus": "no assertion criteria provided",
              "descriptions": [
                {
                  "dateLastEvaluated": "2016-08-31",
                  "classification": "Pathogenic"
                }
              ]
            }
          },
          "classifiedConditions": [
            {
              "condition": "Cleidocranial dysostosis",
              "db": "MedGen",
              "id": "C0008928"
            }
          ]
        }
      ],
      "classifications": {
        "germlineClassification": {
          "reviewStatus": "no assertion criteria provided",
          "classification": "Pathogenic",
          "dateLastEvaluated": "2016-08-31",
          "mostRecentSubmission": "2017-09-09",
          "conditions": [
            {
              "type": "Disease",
              "contributesToAggregateClassification": true,
              "traits": [
                {
                  "id": "820",
                  "name": {
                    "xRefs": [
                      {
                        "db": "Genetic Alliance",
                        "id": "Cleidocranial+Dysplasia/1683"
                      },
                      {
                        "db": "SNOMED CT",
                        "id": "65976001"
                      }
                    ],
                    "value": "Cleidocranial dysostosis"
                  }
                }
              ]
            }
          ]
        }
      },
      "clinicalAssertions": [
        {
          "accession": "SCV000598565"
        }
      ]
    }
  ]
}

large variants:

{
  "clinvar-preview": [
    {
      "chromosome": "17",
      "begin": 150732,
      "end": 14764202,
      "variantType": "copy_number_gain",
      "accession": "VCV000154089",
      "version": "2",
      "recordType": "classified",
      "dateLastUpdated": "2023-10-15",
      "rcvs": [
        {
          "accession": "RCV000142236",
          "version": "6",
          "classifications": {
            "germlineClassification": {
              "reviewStatus": "no assertion criteria provided",
              "descriptions": [
                {
                  "dateLastEvaluated": "2014-03-10",
                  "classification": "Pathogenic"
                }
              ]
            }
          },
          "classifiedConditions": [
            {
              "condition": "See cases"
            }
          ]
        }
      ],
      "classifications": {
        "germlineClassification": {
          "reviewStatus": "no assertion criteria provided",
          "classification": "Pathogenic",
          "dateLastEvaluated": "2014-03-10",
          "mostRecentSubmission": "2015-07-13",
          "conditions": [
            {
              "type": "PhenotypeInstruction",
              "contributesToAggregateClassification": true,
              "traits": [
                {
                  "id": "18728",
                  "name": {
                    "value": "See cases"
                  }
                }
              ]
            }
          ]
        }
      },
      "clinicalAssertions": [
        {
          "accession": "SCV000183512"
        }
      ]
    }
  ]
}

Field	Type	Notes
chromosome	string	Chromosome
begin	integer	start position of variant
end	integer	end of position of variant
refAllele	string
altAllele	string
accession	string	ClinVar ID
version	string	ClinVar version
variantType	string	variant type
recordType	string	record type
dateLastUpdated	string	yyyy-MM-dd
rcvs	array	RCV objects associated to this VCV
classifications	array	classifications for this VCV
clinicalAssertions	array	SCV objects associated to this VCV
isAlleleSpecific	bool	true when the current variant alternate allele matches the ClinVar alternate allele

Variant Types

copy_number_gain
copy_number_loss
deletion
delins
duplication
insertion
inversion
SNV
tandem_duplication

Review Statuses

criteria provided, conflicting classifications
criteria provided, multiple submitters, no conflicts
criteria provided, single submitter
no assertion criteria provided
no classification provided
practice guideline
reviewed by expert panel

classification

Benign
Likely benign
Pathogenic
Uncertain significance
Likely pathogenic
Benign/Likely benign
not provided
conflicting data from submitters
Pathogenic/Likely pathogenic
association
Conflicting classifications of pathogenicity
Pathogenic; risk factor
risk factor
other
drug response
Uncertain significance; Pathogenic/Likely pathogenic
Likely pathogenic, low penetrance
Pathogenic; Affects
Pathogenic, low penetrance
protective
Affects
Benign; other
Conflicting classifications of pathogenicity; other
Conflicting classifications of pathogenicity; association
Uncertain risk allele
Uncertain significance; risk factor
Likely pathogenic; risk factor
Likely benign; association
Likely risk allele
Pathogenic/Likely pathogenic; other
Pathogenic; other
Pathogenic/Likely pathogenic/Pathogenic, low penetrance
Pathogenic/Likely pathogenic; risk factor
Benign/Likely benign; risk factor
Uncertain significance/Uncertain risk allele
Pathogenic; association; protective
protective; risk factor
Benign/Likely benign; other; risk factor
Benign/Likely benign; association
Benign; association
Affects; association; other
Pathogenic; protective
Conflicting classifications of pathogenicity; drug response; other
Conflicting classifications of pathogenicity; drug response
Benign; drug response
Likely pathogenic; other
Conflicting classifications of pathogenicity; protective
Pathogenic/Likely pathogenic; drug response
Benign/Likely benign; other
Likely pathogenic/Likely risk allele
Uncertain risk allele; protective
association not found
Affects; association
Uncertain significance; association
Likely benign; other
Uncertain significance; other
Conflicting classifications of pathogenicity; association; risk factor Pathogenic;
association
Benign; risk factor
Conflicting classifications of pathogenicity; other; risk factor
Pathogenic/Likely risk allele; risk factor
Uncertain significance; drug response
Conflicting classifications of pathogenicity; risk factor
other; risk factor
Pathogenic/Likely pathogenic/Likely risk allele
Likely pathogenic; drug response
Conflicting classifications of pathogenicity; Affects
association; drug response; risk factor
Pathogenic; drug response
Affects; risk factor
Pathogenic; drug response; other
Likely pathogenic; protective
confers sensitivity
Likely pathogenic; association
Benign; Affects
Likely pathogenic; Affects
Uncertain risk allele; risk factor
drug response; risk factor
Pathogenic/Likely risk allele
Likely benign; drug response; other
Benign/Likely benign; drug response
Benign/Likely benign; drug response; other
drug response; other
association; drug response
Pathogenic; confers sensitivity
association; risk factor
Pathogenic/Pathogenic, low penetrance; other
Benign; confers sensitivity
confers sensitivity; other
Likely pathogenic/Pathogenic, low penetrance
Likely benign; risk factor

Building the supplementary files

There are 2 ways of building your own OMIM supplementary files using SAUtils.

The first way is to use SAUtils command's subcommands clinvar. The ClinVar .nsa and .nsi for Illumina Connected Annotations can be built using the SAUtils command's clinvar subcommand.

The second way is to use SAUtils command's subcommands AutoDownloadGenerate. To use AutoDownloadGenerate, read more in SAUtils section.

Using `clinvar` subcommands and source data files

Two input .xml files and a .version file are required in order to build the .nsa and .nsi file. You should have the following files:

ClinVarVCVRelease_00-latest.xml.gz
ClinVarVCVRelease_00-latest.xml.gz.version

The version file is a json file with the following format.

{
  "name": "ClinVar",
  "version": "20240501",
  "description": "A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence",
  "releaseDate": "2024-05-01"
}

You have to adjust the version and release date according to the actual date of the ClinVar.

Here is a sample execution:

dotnet SAUtils ClinVarPreview \
--r ~/References/7/Homo_sapiens.GRCh38.Nirvana.dat\
--vcv ClinVarVCVRelease_00-latest.xml.gz\
--o output
---------------------------------------------------------------------------
SAUtils                                             (c) 2024 Illumina, Inc.
                                                                     3.24.0
---------------------------------------------------------------------------

Parsing XML completed in 14.7 mins.
Sorting and adjusting completed in 4.7 mins.
Writing 2351609 Small Varaints
Chromosome 1 completed in 00:00:57.1
Chromosome 2 completed in 00:01:30.8
Chromosome 3 completed in 00:00:32.9
Chromosome 4 completed in 00:00:21.2
Chromosome 5 completed in 00:00:31.7
Chromosome 6 completed in 00:00:34.6
Chromosome 7 completed in 00:00:27.9
Chromosome 8 completed in 00:00:17.9
Chromosome 9 completed in 00:00:34.0
Chromosome 10 completed in 00:00:26.6
Chromosome 11 completed in 00:00:35.4
Chromosome 12 completed in 00:00:31.5
Chromosome 13 completed in 00:00:22.7
Chromosome 14 completed in 00:00:22.7
Chromosome 15 completed in 00:00:23.7
Chromosome 16 completed in 00:00:39.6
Chromosome 17 completed in 00:00:46.7
Chromosome 18 completed in 00:00:10.2
Chromosome 19 completed in 00:00:32.9
Chromosome 20 completed in 00:00:10.7
Chromosome 21 completed in 00:00:05.3
Chromosome 22 completed in 00:00:11.0
Chromosome X completed in 00:00:19.6
Chromosome Y completed in 00:00:00.1
Chromosome MT completed in 00:00:00.3
Maximum bp shifted for any variant:1
NSA writing completed in 11.5 mins.
Writing 76122 Large Varaints
Writing 76122 intervals to database...
NSI writing completed in 1.1 mins.

Time: 00:32:10.9
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Overview​

Publication

Parsing​

Overall XML to JSON mapping​

Variation fields​

Location fields​

RCVs​

Classifications​

Germline Classification​

Classified Conditions​

Classifications​

Germline Classification​

Conditions​

Clinical Assertions​

Known Issues​

Known Issues

Download URLs​

JSON Output​

Variant Types​

Review Statuses​

classification​

Building the supplementary files​

Using clinvar subcommands and source data files​

Overview

Parsing

Overall XML to JSON mapping

Variation fields

Location fields

RCVs

Classifications

Germline Classification

Classified Conditions

Classifications

Germline Classification

Conditions

Clinical Assertions

Known Issues

Download URLs

JSON Output

Variant Types

Review Statuses

classification

Building the supplementary files

Using `clinvar` subcommands and source data files