Last updated November 12, 2019

README file for ftp://ftp.ncbi.nih.gov/pub/clinvar

This directory contains reports from the ClinVar dataset and documents about
ClinVar development. Sections in this README are divided by type of content.

This directory has a folder for documents related to the collaboration with ClinGen
(http://www.clinicalgenome.org/). For more details, see
http://www.ncbi.nlm.nih.gov/clinvar/docs/review_guidelines.

This README file also documents ClinVar-related data in other directories, such as
ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms, for terminology used by
both GTR and ClinVar.
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen, for gene-disease
relationships related to OMIM

http://www.ncbi.nlm.nih.gov/clinvar/

================================================================================
SUBMISSIONS
================================================================================
Details about how to submit are provided at this site:
http://www.ncbi.nlm.nih.gov/clinvar/docs/submit/

--------------------------------------------------
clinvar_submission.xsd
--------------------------------------------------

If you have any questions about submitting data to ClinVar as an XML file, please
contact us via [email protected]
This is the .xsd file for validating records submitted to ClinVar as xml.

------------------------------------------------------------
history of the versions of clinvar_submission.xsd
subdirectory xsd_submission
------------------------------------------------------------
This subdirectory archives different versions of the submission xsd. The current
one is also accessible as clinvar_submission.xsd

--------------------------------------------------
submission_templates
subdirectory ftp://ftp.ncbi.nih.gov/pub/clinvar/submission_templates
--------------------------------------------------
This subdirectory contains excel spreadsheets that can be used to
submit data to ClinVar.

There are two templates in this directory:

SubmissionTemplate.xlsx
SubmissionTemplateLite.xlsx

SubmissionTemplate.xlsx is the standard submission template.

SubmissionTemplateLite.xlsx is simpler, and is designed for

submissions with less supporting evidence.

================================================================================
EXTRACTS OF CLINVAR DATA
================================================================================
ClinVar data are provided for download as extracts in xml, vcf and tab-delimited
formats in the directories described below.

-------------------------------------------------
Updates
-------------------------------------------------
Data on the ftp site are updated monthly and weekly.
Please note on each file how when the data are refreshed.

Monthly: usually the first Thursday of the month.

A copy is also made to the archive sub-directory.

Weekly: usually on Mondays

XML: Weekly releases are not archived, and accumulate in the
weekly_release subdirectory until the next monthly release.
tab-delimited: The latest version is retained in the tab-
delimited path.
The archive subdirectory retains the copy
consistent with the monthly release.

-------------------------------------------------
clinvar_public.xsd
-------------------------------------------------
The schema for the export version of the XML
clinvar_public.xsd Link to the current version such as
/xsd_public/clinvar_public_1.5.xsd

------------------------------------------------------------
history of the versions of clinvar_submission.xsd
subdirectory xsd_public
------------------------------------------------------------
This subdirectory archives different versions of xsd used to validate ClinVar's
comprehensive export as xml. The current one is also accessible as
clinvar_submission.xsd

The version number is represented in the file name.

----------------------------------------
release_notes
----------------------------------------
The release_notes subdirectory contains reports of the differences between
versions of clinvar_public.xsd

================================================================================
NAMES OF PHENOTYPES
================================================================================

--------------------------------------------------
disease_names
--------------------------------------------------

This document is updated daily, and is provided to report the names and
identifiers used in GTR and ClinVar. Please note there may be more than one
line per condition, when a name is used by more than one source. This
differs from the gene_condition_source_id file because it is comprehensive,
and does not require knowledge of any gene-to-disease relationship.
 Tab-delimited file with the following 7 fields:

DiseaseName: The name preferred by GTR and ClinVar

SourceName: Sources that also use this preferred name
ConceptID: The identifier assigned to a disorder associated with this
gene. If the value starts with a C and is followed by
digits,
the ConceptID is a value from UMLS; if a value begins with
CN,
it was created by NCBI-based processing.
SourceID: Identifier used by the source reported in column 2
DiseaseMIM: MIM number for the condition.
LastUpdated: Last time this record was modified by NCBI staff
Category: Category of disease (as reported in ClinVar's XML), one of:
- Blood group
- Disease
- Finding
- Named protein variant
- Pharmacological response
- phenotype instruction

--------------------------------------------------
gene_condition_source_id
--------------------------------------------------

This document is updated daily, and is provided to report gene-disease

relationships used in ClinVar, Gene, GTR and MedGen.
The sources of information for the gene-disease relationship include OMIM,
GeneReviews, and a limited amount of curation by NCBI staff.
The scope of disorders reported in this file is a subset of the disease_names
file because a gene-to-disease relationship is required.
Tab-delimited file with the following fields:

GeneID: The NCBI GeneID

GeneSymbol: The preferred symbol corresponding to the GeneID
ConceptID: The identifier assigned to a disorder associated with this
gene. If the value starts with a C and is followed by
digits,
the ConceptID is a value from UMLS; if a value begins with
CN, it was created by NCBI-based processing
DiseaseName: Full name for the condition
SourceName: Sources that use this name
SourceID: The identifier used by this source
DiseaseMIM: MIM number for the condition
LastUpdated: Last time this record was modified by NCBI staff

--------------------------------------------------
ConceptID_history.txt
--------------------------------------------------
--Added to the directory October 24, 2012

This document is updated daily, and is provided to help track changes in

identifiers assigned to phenotypes over time. The ConceptID values in the
first column are no longer active, and are either discontinued (the value in
column 2 is 'No longer reported', or replaced by a record with a different
identifier. That replacement may result either because of a merge (one record
becoming secondary to another) or because of a change in numbering, usually
because an identifier assigned by NCBI (starting with CN) is now thought to be
represented by a ConceptID from UMLS (starting with C followed by numerals).

Previous ConceptID the outdated identifier

Current ConceptID the current identifier
Date of Action the date this change occurred

--------------------------------------------------
dbGaP_frequency_study_list
--------------------------------------------------
--Added to the directory September 29, 2015

Text and html files reporting the studies in dbGaP that were assessed for single
nucleotide variants reported in ClinVar.
dbGaP_frequency_study_list.html
dbGaP_frequency_study_list.txt

================================================================================
SUBDIRECTORIES
================================================================================
community files generated in the initial design of ClinVar
presentations slides or other documents about ClinVar
submission_templates templates for submission by spreadsheet
tab_delimited flattened tabular data summaries of several types
-----------------------VCF------------------------
See the README specific to ClinVar's VCF files:
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/README_VCF.txt
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/README_VCF.txt
--------------------------------------------------
xml An extraction of data in ClinVar as xml
The xsd for the export version of the XML is clinvar_public.xsd
For more details about the files in the xml directory, please refer to
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/_README

==================================================
tab_delimited sub-directory

ClinVar makes every attempt to retain backward compatibility in its information

products.
If changes are made to these tab-delimited files, new columns are usually added to
the end.
If, however, a column needs to be removed, the names of the remaining column
headers will be stable.

Most of the files in this directory are generated weekly, usually on Mondays.
Not all of the files in this directory are archived, so please note the for each
file whether
monthly versions are copies to the archive subdirectory the first of each month.

--------------------------------------------------------------------------------
1. gene_specific_summary
--------------------------------------------------------------------------------
Generated weekly
Archived monthly ( first Thurday of each month)

Although this report is generated each week, it is currently based on statistics

that are captured the first day of each month.
Therefore there will be some discrepancies between what is reported in this file
and what may be viewed interactively on the web.

A tab-delimited report, for each gene, of the number of submissions and the number
of different variants (alleles).
Because some variant-gene relationships are submitted, and some are calculated from
overlapping annotation, in January of 2015, the report was modified to indicate
when the gene-variant relationship was submitted.

Symbol Gene symbol (if officially named, from HGNC, else from
NCBI's Gene database)
GeneID Unique identifier from NCBI's Gene database
Total_submissions Total submissions to ClinVar with variants in/overlapping
this gene
Total_alleles Number of alleles submitted to ClinVar for this gene
Submissions_reporting_this_gene
Subset of the total submissions that also reported the gene
Alleles_reported_Pathogenic_Likely_pathogenic
Number of variants reported as pathogenic or likely
pathogenic
Excludes structural variants that may overlap a gene
Gene_MIM_Number The MIM number for this gene
Number_Uncertain Submissions with an interpretation of 'Uncertain
significance'
Number_with_conflicts Number of VariationIDs for this gene with conflicting
interpretations
--------------------------------------------------------------------------------
2. variant_summary.txt
--------------------------------------------------------------------------------
Generated weekly
Archived monthly (first Thurday of each month)

A tab-delimited report based on each variant at a location on the genome for which
data have been submitted to ClinVar.
The data for the variant are reported for each assembly, so most variants have a
line for GRCh37 (hg19) and another line for GRCh38 (hg38).

Please note: Beginning in October 2016, this file was modified to restrict
reporting to attributes of an AlleleID, not a mixture of AlleleID and VariationID.
The modifications were announced in our September 2016 release notes:
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/release_notes/20160901_data_release_notes.pd
f.

The last file that reported VariationID was

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/archive/variant_summary_2016-
09.txt.gz
The first with the new set of columns is
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/archive/variant_summary_2016-
10.txt.gz
Content that used to be in this file may be found in

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/hgvs4variation.txt.gz

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz

Please note: Beginning in November 2019, the values for referenceAllele and
alternateAllele are being written according to the VCF
standard. For single nucleotide variants there was no change in the
value.
 See also the authoritative file for identifiers assigned to genes
represented by NCBI, namely:

ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz

AlleleID integer value as stored in the AlleleID field in ClinVar

(//Measure/@ID in the XML)
Type character, the type of variant represented by the AlleleID
Name character, ClinVar's preferred name for the record with this
AlleleID
GeneID integer, GeneID in NCBI's Gene database, reported if there
is a single gene, otherwise reported as -1.
GeneSymbol character, comma-separated list of GeneIDs overlapping the
variant
HGNC_ID string, of format HGNC:integer, reported if there is a
single GeneID. Otherwise reported as '-'
ClinicalSignificance character, comma-separated list of aggregate values of
clinical significance calculated for this variant
If the value is 'no interpretation for the single variant',
this allele was submitted to
ClinVar as part of a haplotype or genotype, and its specific
significance has not been submitted to ClinVar.
NOTE: Now that the aggregate values of clinical significance
give precedence to records
with assertion criteria and evidence, the values in
this column may appear to be in
conflict with the value reported in ClinSigSimple.
ClinSigSimple integer, 0 = no current value of Likely pathogenic or
Pathogenic
1 = at least one current record submitted with an
interpretation of Likely pathogenic or
Pathogenic (independent of whether that record
includes assertion criteria and evidence).
-1 = no values for clinical significance at all for
this variant or set of variants; used for
the "included" variants that are only in
ClinVar because they are included in a
haplotype or genotype with an interpretation
NOTE: Now that the aggregate values of clinical significance
give precedence to records with
assertion criteria and evidence, the values in this
column may appear to be in conflict with the
value reported in ClinicalSignificance. In other
words, if a submission without assertion criteria and
evidence interpreted an allele as pathogenic, and
those with assertion criteria and evidence interpreted
as benign, then ClinicalSignificance would be reported
as Benign and ClinSigSimple as 1.
LastEvaluated date, the latest date any submitter reported clinical
significance
RS# (dbSNP) integer, rs# in dbSNP, reported as -1 if missing
nsv/esv (dbVar) character, the NSV identifier for the region in dbVar
RCVaccession character, list of RCV accessions that report this variant
PhenotypeIDs character, list of identifiers for phenotype(s) interpreted
for this variant
PhenotypeList character, list of names corresponding to PhenotypeIDs
Origin character, list of all allelic origins for this variant
OriginSimple character, processed from Origin to make it easier to
distinguish between germline and somatic
Assembly character, name of the assembly on which locations are based
ChromosomeAccession Accession and version of the RefSeq sequence defining the
position reported in the start and stop columns.
Please note some of these accessions may be for sub-
chromosomal regions.
Chromosome character, chromosomal location
Start integer, starting location, in pter->qter orientation
Stop integer, end location, in pter->qter orientation
ReferenceAllele The reference allele according to the vcf standard.
AlternateAllele The alternate allele according to the vcf standard.
Cytogenetic character, ISCN band
ReviewStatus character, highest review status for reporting this measure.
For the key to the terms,
and their relationship to the star graphics ClinVar
displays on its web pages,
see
http://www.ncbi.nlm.nih.gov/clinvar/docs/variation_report/#interpretation
Note also that 'no
interpretation for the single variant' is used for AlleleIDs in ClinVar
that were submitted as part
of the definition of a complex allele, but not interpreted
individually.
NumberSubmitters integer, number of submitters describing this variant
Guidelines character, ACMG only right now, for the reporting of
incidental variation in a Gene
enumerates whether the guideline is from 2013 (ACMG2013,
PubMed 23788249) or 2016 (ACMG2016, PubMed 27854360)
(NOTE: if ACMG, not a specific to the AlleleID but
to the Gene in which the AlleleID is found)
TestedInGTR character, Y/N for Yes/No if there is a test registered as
specific to this variant
in the NIH Genetic Testing Registry (GTR)
OtherIDs character, list of other identifiers or sources of
information about this variant
SubmitterCategories coded value to indicate whether data were submitted by
another resource (1), any other type of source (2) or both (3)
VariationID The identifier ClinVar uses specific to the AlleleID. Not
all VariationIDS that may be related to
the AlleleID are reported in this file. For a
comprehensive mapping of AlleleID to VariationID,
please use
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variation_allele.txt.gz.
Note also that some of the values
for VariationID are not supported in the current
default web display, but will
be reported from ClinVar 2.0 as current seen from our preview site.

--------------------------------------------------------------------------------
3. cross_references.txt
--------------------------------------------------------------------------------
Generated weekly
Not archived

A tab-delimited report based on each variant in ClinVar, providing identifiers in

other databases and when those data were last updated. This file is based on
AlleleID rather than VariationID for complex alleles, so it corresponds to a unique
genomic location.
NOTE: this file is preliminary and currently includes only identifiers in dbSNP and
dbVar. Identifiers from more databases will be added in the future.

AlleleID integer value as stored in the AlleleID field

in ClinVar (//Measure/@ID in the XML)
Database name of the database
ID identifier used by that database
last_updated date the identifier /AlleleID relationship was
created or last updated

--------------------------------------------------------------------------------
4. var_citations.txt
--------------------------------------------------------------------------------
Generated weekly
Not archived

A tab-delimited report of citations associated with data in ClinVar, connected to

the AlleleID, the VariationID, and either rs# from dbSNP or nsv in dbVar.

AlleleID integer value as stored in the AlleleID field in

ClinVar (//Measure/@ID in the XML)
VariationID The identifier ClinVar uses to anchor its default
display. (in the XML, //MeasureSet/@ID)
rs rs identifier from
dbSNP, null if missing
nsv nsv identifier from dbVar,
null if missing
citation_source The source of the citation, either
PubMed, PubMedCentral, or the NCBI Bookshelf
citation_id The identifier used by that source

--------------------------------------------------------------------------------
5. summary_of_conflicting_interpretations.txt
--------------------------------------------------------------------------------
Generated weekly
Archived monthly ( first Thurday of each month)

This file first became available in January, 2016. It replaces

summary_of_conflicting_data.txt (documented below) and differs in that
a. It is limited to differences in interpretation (i.e. does not report
differences in the phenotype being interpreted)
b. Reports all pairwise differences, so that if submitter a differs from
submitters b and c, and submitter b differs from c, a-b, a-c, b-c will all be
reported instead of just a-b and a-c
c. Reports fewer columns

Gene_Symbol If in a gene, its symbol

NCBI_Variation_ID The identifier ClinVar uses to anchor its
default display. (in the XML, //MeasureSet/@ID)
ClinVar_Preferred The preferred description ClinVar uses for
this VariationID
Submitter1 Name of this submitter
Submitter1_SCV Accession assigned to this
submission
Submitter1_ClinSig Clinical signficance asserted by this
submitter
Submitter1_LastEval Date last evaluated by this submitter
Submitter1_ReviewStatus Review status of this submission
Submitter1_Sub_Condition Submitted name of condition
Submitter1_Description Description of the interpretation
Submitter2 Name of this submitter
Submitter2_SCV Accession assigned to this submission
Submitter2_ClinSig Clinical significance asserted by
this submitter
Submitter2_LastEval Date last evaluated by this submitter
Submitter2_ReviewStatus Review status of this submission
Submitter2_Sub_Condition Submitted name of condition
Submitter2_Description Description of the interpretation
Rank_diff Rank value assigned to the differences in
interpretation:
-1: one of the interpretations is not in
the set of Pathogenic, Likely pathogenic, Uncertain significance, Likely benign,
Benign
0: difference in phenotype only
1-4, difference when both interpretations
are in the set of Pathogenic, Likely pathogenic, Uncertain significance,
Likely benign, Benign, where 4 is
most divergent
Conflict_Reported yes or no. Useful to supplement the Rank_diff
column when Rank_diff = 1 but a conflict is still reported.
Variant_Type the type of variant being described
Submitter1_Method the collection method(s) reported by this
submitter
Submitter2_Method the collection method(s) reported by this
submitter
--------------------------------------------------------------------------------
6. hgvs4variation.txt.gz
--------------------------------------------------------------------------------
Updated weekly
Not archived

A compressed report of HGVS expressions ClinVar reports per VariationID and

AlleleID. These are broadly categorized by type, based on the reference sequence
(coding, genomic, non-coding, protein, RNA) and on the complexity of the submission
represented by the VariationID (CompoundHeterozygote, Distinct chromosomes,
Haplotype, Phase unknown).

The header of the file explains the columns, which include the VariationID, the
AlleleID, the type and the HGVS expression. The NCBI GeneID and GeneSymbol are
included for ready filtering of lines in the file by gene. The assembly is provided
for the HGVS expressions based on chromosome sequences; otherwise the assembly is
reported as 'na'.
HINT: Please note that for human, the accession of the RefSeq representing each
chromosome indicates the chromosome being represented. In other words, NC_000001 is
for chromosome 1, NC_000002 is for chromosome 2, ... NC_000023 is for X, and
NC_000024 is for Y.
In the December release, 3 columns were added to support those wishing to identify
which HGVS expressions are used for naming, which HGVS expressions were provided
explicitly by a submitter, and which are based on RefSeqs that are reference
standards on RefSeqGenes.
--------------------------------------------------------------------------------
7. variation_allele.txt
--------------------------------------------------------------------------------
Updated weekly
Not archived

Mapping of ClinVar's VariationID (used to build the URL on the web site) and the
AlleleIDs assigned to each simple variant.
1. VariationID: the identifier assigned by ClinVar and used to build the
URL, namely https://ncbi.nlm.nih.gov/clinvar/VariationID
2. Type: Types of VariationID include Variant (simple variant),
Haplotype, CompoundHeterozygote, Complex, Phase unknown, Distinct chromosomes
3. AlleleID: the integer identifier assigned by ClinVar to each
simple allele
4. Interpreted: _yes_ indicates an interpretation was submitted about
the VariationID specifically,
_no_ indicates that information about the VariationID
was submitted as a component of a different record.

--------------------------------------------------------------------------------
8. submission_summary.txt
--------------------------------------------------------------------------------
Generated weekly
Archived monthly (first Thurday of each month)

Overview of interpretation, phenotypes, observations, and methods reported in

each current submission

1. VariationID: the identifier assigned by ClinVar and used to build

the URL, namely https://ncbi.nlm.nih.gov/clinvar/VariationID
2. ClinicalSignificance: interpretation of the variation-condition
relationship
3. DateLastEvaluated: the last date the variation-condition relationship
was evaluated by this submitter
4. Description: an optional free text description of the basis of the
interpretation
5. SubmittedPhenotypeInfo: the name(s) or identifier(s) submitted for the
condition that was interpreted relative to the variant
6. ReportedPhenotypeInfo: the MedGen identifier/name combinations ClinVar uses
to report the condition that was interpreted. 'na' means there is no public
identifier in MedGen for the condition.
7. ReviewStatus: the level of review for this submission, namely
http://www.ncbi.nlm.nih.gov/clinvar/docs/variation_report/#review_status
8. CollectionMethod: the method by which the submitter obtained the
information provided
9. OriginCounts: the reported origin and the number of observations
for each origin
10. Submitter: the submitter of this record
11. SCV: the accession and current version assigned by ClinVar
to the submitted interpretation of the variation-condition relationship
12. SubmittedGeneSymbol: the symbol provided by the submitter for the gene
affected by the variant. May be null.

--------------------------------------------------------------------------------
9. allele_gene.txt
--------------------------------------------------------------------------------
Updated weekly
Not archived

Reports per ClinVar's AlleleID, the genes that are related to that gene and how
they are related. The values for category are:

asserted, but not computed: Submitted as related to a gene, but not within
the location of that gene on the genome
genes overlapped by variant The gene and variant overlap
near gene, downstream Outside the location of the gene on the
genome, within 5 kb
near gene, upstream Outside the location of the gene on the
genome, within 5 kb
within multiple genes by overlap The variant is within genes that overlap on
the genome. Includes introns.
within single gene The variant is in only one
gene. Includes introns.

AlleleID: the integer identifier assigned by ClinVar to

each simple allele
GeneID: integer, GeneID in NCBI's Gene database
Symbol character, Symbol preferred in NCBI's Gene
database. Is the symbol from HGNC when available
Name character, full name of the gene
GenesPerAlleleID integer, number of genes related to the allele
Category character, type of allele-
gene relationship
Source character, was the relationship submitted or
calculated?

10. organization_summary.txt
updated weekly
not archived

organization the name of the lab and the institution of

which it is part
organization ID the id used in ClinVar and GTR; often reported
as OrgID;
append to
https://www.ncbi.nlm.nih.gov/clinvar/submitters to review more details
institution type type of organization
street address street address
country country
number of ClinVar submissions number of submission to ClinVar
date last submitted last date on a public submission from this
organization
maximum review status the 'most stars' valid for any submission from
this organization
collection methods comma-delimited list of methods used to
determine information for the submission
novel and updates values are novel, novel and updates. The
latter indicates the submitter has provided updates.
clinical significance categories submitted
list of types of interpretations from this
organization
number of submissions from clinical testing
number of submissions for the list of
categories in 'collection methods'
number of submissions from research
number of submissions for the list of
categories in 'collection methods'
number of submissions from literature only
number of submissions for the list of
categories in 'collection methods'
number of submissions from curation
number of submissions for the list of
categories in 'collection methods'
number of submissions from phenotyping
number of submissions for the list of
categories in 'collection methods'

11. special_requests subdirectory

This path contains files that were requested by more than one user. The reports are
not kept current, but if the contents are considered useful, they may be converted
to production level and updated regularly. For more details, see the README.txt
file in that path.

================================================================================
VALIDATING FILE DOWNLOADS
================================================================================
We are providing md5 checksum files to validate file downloads to ensure your ftp
transfer is complete. If you are unfamiliar with md5 it is a string of letters and
numbers that act as a fingerprint for a file. When you download the file generate
an md5 hash and compare to the value in our md5 checksum file to ensure your
download has the entire file. We are currently providing md5 files for some of the
tab_delmited files and the ClinVarFullRelease XML file. After you download a file,
use a utility to create a checksum value and compare it to the one we provide. In
the linux enviroment, the utility is likely md5sum. There is freeware available for
tools in other environments.

================================================================================
RELATED SITES
================================================================================
--------------------------------------------------
Gene-disease relationships
--------------------------------------------------
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen

This file, completely documented in ftp://ftp.ncbi.nih.gov/gene/README, maintains

information about gene-disease relationships inferred from gene-variation and
variation-disease relationships or reported by OMIM.

--------------------------------------------------
standard terms
--------------------------------------------------
ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/

This directory contains terms used by ClinVar and GTR in specified categories.
Cross-references to the term in other databases may also be provided.

================================================================================
ClinGen
================================================================================
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/ClinGen/

ClinVar is an active participant in the ClinGen project.

(http://clinicalgenome.org/)
As part of that collaboration, ClinVar requests that submitters wishing to be
identified as an expert panel provide documentation about their their methods of
determining Clinical Significance. The form to be completed is provided in this
directory.

================================================================================
MISCELLANEOUS
================================================================================
--------------------------------------------------
2013.1-hgmd-public.tsv
--------------------------------------------------
This file was removed June 19, 2013 on request from HGMD.

vcf
This path was removed to make explicit the difference between VCF files on GRCh37
and GRCh38.
It was replaced with vcf_GRCh37 and vcf_GRCh38

======================================================================
Partial revision history
======================================================================
December 3, 2014: Added the file /tab_delimited/summary_of_conflicting_data.txt
January 12, 2015: Documented the changes to gene_specific_summary.txt and
explained the new directory structure
for vcf files.
September 10, 2015: Documented providing md5 files.
April 7, 2016: Discontinued generating summary_of_conflicting_data.txt
The historical reports are maintained in the archive directory
(ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/archive/)

It was defined as below:

Generated monthly, the first Thursday of the month
A tab-delimited report based on variants in ClinVar, for which information has been
provided by more than one submitter, and for which there is inconsistency in
reporting phenotype or interpretation. The file includes some basic information
about the variant, and then describes what each submitter said for which a
discrepancy was noted. Although generated primarily for the submitter, or groups
reviewing evidence supporting variant assessments, this file may be of interest to
others as well. Please note *all* data conflicts are reported. To focus on a
subset of interest, we suggest you use either the Rank_diff or Conflict_Reported
columns. For example, look for rows in the report where Rank_diff >=2 for
Conflict_Reported is 'yes'.

Gene_Symbol If in a gene, its symbol

NCBI_Variation_ID The identifier ClinVar uses to anchor its
default display. (in the XML, //MeasureSet/@ID)
NCBI_AlleleID The identifier ClinVar uses to define an
allele. (in the XML, //Measure/@ID)
HGVS The default HGVS expression for this variant
Submitter1 Name of this submitter
Submitter1_ID Identifier for this variant
provided by this submitter, or constructed by NCBI for the submitter
Submitter1_SCV Accession assigned to this
submission
Submitter1_Definition Variant as defined by this
submitter (currently missing for those not submitted by HGVS)
Submitter1_ClinSig Clinical significance asserted by this
submitter
Submitter1_LastEval Date last evaluated by this submitter
Submitter1_AssertionMethod Assertion method
Submitter1_Sub_Condition Submitted name of condition
Submitter1_Calc_Condition Name ClinVar uses for this condition
Submitter1_Description Description of the interpretation
Submitter2 Name of this submitter
Submitter2_ID Identifier for this variant provided by this
submitter, or constructed by NCBI for the submitter
Submitter2_SCV Accession assigned to this submission
Submitter2_Definition Variant as defined by this submitter
(currently missing for those not submitted by HGVS)
Submitter2_ClinSig Clinical significance asserted by
this submitter
Submitter2_LastEval Date last evaluated by this submitter
Submitter2_AssertionMethod Assertion method
Submitter2_Sub_Condition Submitted name of condition
Submitter2_Calc_Condition Name ClinVar uses for this condition
Submitter2_Description Description of the interpretation
Rank_diff Rank value assigned to the differences in
interpretation:
-1: one of the interpretations is not in
the set of Pathogenic, Likely pathogenic, Uncertain significance, Likely benign,
Benign
0: difference in phenotype only
1-4, difference when both interpretations
are in the set of Pathogenic, Likely pathogenic, Uncertain significance,
Likely benign, Benign, where 4 is
most divergent
Conflict_Reported yes or no. Useful to supplement the Rank_diff
column when Rank_diff = 1 but a conflict is still reported.
Variant_Type the type of variant being described

August 4, 2016: Added documentation for several new files in the tab-
delimited subdirectory
* hgvs4variation.txt.gz
* submission_summary.txt
* variation_allele.txt
Added explanation of numbering systems for locations in VCF
vs. all other reports

September 24, 2016: Added documentation for the allele_gene files in the tab-
delimited directory
November 9, 2016: Corrected documentation for variant_summary that should have
been included in the October update.
December 9, 2016: Added SubmittedGeneSymbol to the description of
submission_summary.txt, and updated the description of hgvs4variation.txt.gz
January 19, 2017 Corrected inconsistent definition of NumberSubmitters in
variant_summary.txt
November 30, 2017 Modification to summary_of_conflicting_interpretations.txt
February 20, 2019 Added documentation of organization_summary.txt
November 12, 2019 Noted change in reporting referenceAllele and
alternateAllele in variant_summary.txt; added more information about releases.