Representation of clinical significance in ClinVar and other variation resources at NCBI

Clinical significance on ClinVar submissions (SCV)

Standardizing representation

ClinVar uses standard terms for clinical significance recommended by an authoritative source when available. These standards include:

Other non-standard terms are also used to meet submitter needs. ClinVar plans to add standard terms for other scenarios (e.g. somatic, pharmacogenomic, and mitochondrial variants) when they are available.

Options for clinical significance

The list of terms currently used by both ClinVar and GTR is reported on GTR's ftp site: ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/Clinical_significance.txt.  The following table lists these options for clinical significance for an individual submission (SCV) in ClinVar and  guidance for when each term should be used.

Clinical significance value Guidance for use in ClinVar SCV records
Benign As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Likely benign As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Uncertain significance As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Likely pathogenic As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Pathogenic

As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.

Variants that have low penetrance may be submitted as "Pathogenic"; please also include information about the penetrance in a "Comment on clinical significance".

drug response A general term for a variant that affects a drug response, not a disease. We anticipate adding more specific drug response terms based on a recommendation by CPIC.
association For variants identified in a GWAS study and further interpreted for their clinical significance.
risk factor For variants that are interpreted not to cause a disorder but to increase the risk.
protective For variants that decrease the risk of a disorder, including infections.
Affects For variants that cause a non-disease phenotype, such as lactose intolerance.
conflicting data from submitters Only for submissions from a consortium, where groups within the consortium have conflicting intepretations of a variant but provide a single submission to ClinVar.
other If ClinVar does not have the appropriate term for your submission, we ask that you submit "other" as clinical significance and contact us to discuss if there are other terms we should add.

not provided

For submissions without an interpretation of clinical significance. The primary goal of ClinVar is to archive reports of clinical significance of variants. Therefore submissions with a clinical significance of "not provided" should be limited to:

  • "literature only" submissions that report a publication about the variant, without interpreting the clinical significance
  • "research" submissions that provide functional significance (e.g. undetectable protein level) but no interpretation of clinical significance
  • "clinical testing" or "phenotyping only" submissions from clinics or physicians that provide additional information about individuals with the variant, such as observed phenotypes, but do not interpret the clinical significance
'-' This value may not be submitted. It is used in the file variant_summary.txt.gz in the path  ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/. This file reports  '-' in the ClinicalSignificance column for an allele that was submitted to ClinVar only in combination with another allele (e.g. a submission with an interpretation of a haplotype or a compound heterozygote) and was not interpreted explictly.  ClinVar thus has no interpretation specific to that allele.  To find the the interpretation that includes that allele, you can query ClinVar by the AlleleID, e.g. https://www.ncbi.nlm.nih.gov/clinvar/?term=38420[alleleid].

Clinical significance and mode of inheritance

Submitters should provide a value for clinical significance in the context of a submitted mode of inheritance. Thus a disease-causing variant for a recessive disorder should be reported as Pathogenic, not Benign, even though the single copy will not cause disease.

When a submitter specifies a mode of inheritance, that value is displayed on the variant page on the "Clinical assertions" tab in parentheses in the Conditions column, as in this example.

Source of the interpretations of medical relevance

The values of clinical significance ClinVar represents are not calculated by NCBI; the interpretation of the relationship of variation to a condition is provided only by the submitter. The submitted clinical significance value is reflected in the submitter's record (represented by an accession starting with SCV) and is used to calculate conflicts in interpretation when all submissions about the same variation and condition are aggregated (into a record with an accession starting with RCV).

  • In other words, ClinVar staff do NOT curate submitted interpretations to determine if they are correct. 
  • If you believe an interpretation is in error,  you are invited to submit your data with your interpretation so the conflict will be noted and external groups such as ClinGen can focus on evaluation of all evidence.

There are two exceptions to the statement that ClinVar processes only what is explicitly submitted about clinical significance.

1. Data provided by OMIM do not include an explicit interpretation of clinical significance. When ClinVar processes data from OMIM for submission, we map the disorders or phenotypes associated with each record into clinical significance values according to the following guidelines provided by OMIM:

Key Word(s) in Title of OMIM Entry or description in OMIM's genemap file Clinical Significance
Rules for Assigning Clinical Significance Values to OMIM's Allelic Variants
non-disease Affects (implemented in the October, 2015 release)
named protein variants other, unless curated by NCBI staff to connect to a condition or phenotype
"POLYMORPHISM" Benign
"PROTECTION AGAINST" protective
"QUANTITATIVE TRAIT" association
"RESPONSE" not "SUSCEPTIBILITY" drug response
"SOMATIC" not "RESPONSE" pathogenic (implemented in the September, 2014 release)

"SUSCEPTIBILITY TO"
"SUSCEPTIBILITY" followed by a numeral
"MODIFIER OF" not "RESPONSE"

risk factor

Note: For the case of variants in BRCA1 and BRCA2 related to breast cancer, OMIM asserted these should be treated as pathogenic.

"VARIANT OF UNKNOWN SIGNIFICANCE" Uncertain significance, also reviewed as time permits to determine if there is a disorder for which the variant has an uncertain significance.
contains an identifier from dbSNP Reviewed as time permits to determine if the accompanying text is reporting an association, a polymorphism, or a causative variant.
key title word(s) that do not match any of the above Pathogenic

2. In some early submissions, some submitters provided clinical significance using their own term list. In this case, the SCV record reflects the submitted clinical significance value, but ClinVar staff worked with the submitter to map the submitted term to one of NCBI's standard terms. This standardization is necessary to support calculation of conflicts of interpretation. Current submissions to ClinVar must use the list of clinical significance terms that ClinVar processes.

 

Clinical significance on ClinVar aggregate records (RCV or Variation reports)

The values of clinical significance reported in ClinVar RCV records and on the web-based Variation report are based on the clinical significance values for all the SCVs aggregated for the RCV record or the Variation ID. 

Representing conflicts in interpretation

The clinical significance terms recommended by ACMG/AMP use five levels to describe pathogenicity. Differences in interpretation among submitters only within those five levels  are reported as a conflict using the phrase 'Conflicting interpretations of pathogenicity'. Other values of clinical significance (in the table above) are not considered to be conflicts.

  • RCV records
    • Starting in May 2018, conflicts on RCV records are reported between three levels or pathogencity, i.e. Benign or Likely benign vs Uncertain significance vs Pathogenic or Likely pathogenic.
    • Before May 2018, any conflict within the five terms of pathogenicity was reported as a conflict on an RCV record. e.g. Pathogenic and Likely pathogenic were reported as a conflict.
  • Variation reports
    • Conflicts are reported between three levels of pathogenicity, i.e. Benign or Likely benign vs Uncertain significance vs Pathogenic or Likely pathogenic.
    • If the conflict is between 'Pathogenic' and 'Likely pathogenic' or between 'Benign' and 'Likely benign', ClinVar reports the term 'Pathogenic/Likely pathogenic' or 'Benign/Likely benign', respectively, rather than 'conflicting interpretations of pathogenicity'. 
  • If ClinVar aggregates submissions from groups that provided a standard term not recommend by ACMG/AMP (e.g. drug response), then those values are reported after the ACMG/AMP-based interpretation (see the table below).
  • Conflicts on aggregate records are reported in the XML extraction, the tab-delimited variant_summary.txt file, and on the web pages.
  • When there is a submission from an Expert panel or from a group providing practice guidelines, only the interpretation from that group is reported in the aggregate record, even if other submissions provide different interpretations.  The assertion on the SCV record from each submitter is not changed.
  • Combination of values from different submitters Reported as
    Pathogenic and Likely pathogenic Pathogenic/LikelyPathogenic
    (Pathogenic or Likely pathogenic or Benign or Likely benign)  AND Uncertain significance

    Conflicting interpretations of pathogenicity

    (Pathogenic or Likely pathogenic) AND (Benign or Likely benign)

    Conflicting interpretations of pathogenicity

    Benign and Likely benign Benign/Likely benign
    Any single ACMG value AND any non-ACMG value, e.g. Uncertain significance and risk factor Uncertain significance, risk factor
    Conflicting ACMG values AND any non-ACMG value, e.g. Pathogenic and Uncertain significance and risk factor Conflicting interpretations of pathogenicity, risk factor

    No ACMG value AND multiple non-ACMG values, e.g.  Drug response and risk factor

    drug response, risk factor
    A consortium does not agree on which ACMG assessement is valid conflicting data from submitters

    Representation in other NCBI variation resources

    Variation Reporter

    The values of clinical significance used in Variation Reporter are based on the aggregation from the Variation report.

    ASN.1 files

    ASN.1 files from NCBI with clinical variant annotation use a different set of clinical significance terms than those displayed in ClinVar and VCF, with the following mapping:

    ASN.1 terms ClinVar and VCF
    0 – unknown Uncertain significance
    1 – untested not provided (includes the cases where data are not available or unknown)
    2 - non-pathogenic Benign
    3 - probable-non-pathogenic Likely benign
    4 - probable-pathogenic Likely pathogenic
    5 – pathogenic Pathogenic
    6 - drug-response drug response
    7 – histocompatibility histocompatibility
    255 - other other
      confers sensitivity
      risk factor
      association
      protective
      Affects
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Last updated: 2017-07-07T16:43:07-04:00