ClinVar

HGVS Expressions in ClinVar

This document summarizes the elements used in ClinVar's XML to represent different types of HGVS expressions.  For submission ( https://ftp.ncbi.nlm.nih.gov/pub/clinvar/clinvar_submission.xsd ), the element HGVS is sufficient, but for public reporting these are stratified into more specific types ( https://ftp.ncbi.nlm.nih.gov/pub/clinvar/clinvar_public.xsd ).

HGVS, genomic, RefSeqGene (g.)

A valid HGVS expression on the RefSeqGene. If there are overlapping RefSeqGenes and an allele is represented on multiple RefSeqGenes, then ClinVar reports the HGVS expression on the RefSeqGene that represents the gene about which there is an asserted relationship between variation and the disorder.

HGVS, genomic, LRG  (g.)

A valid HGVS expression on the LRG. If there are overlapping LRGs and an allele is represented on multiple LRGs , then ClinVar reports the HGVS expression on the LRG that represents the gene about which there is an asserted relationship between variation and the disorder.

HGVS, genomic, top level (g. or m.)

A valid HGVS expression based on top-level genomic sequences (assembled chromosomes, mitochondrion,  or alternate loci or patches).

HGVS, genomic (g.)

A valid HGVS expression on a genomic sequence but not included in any of the above because either:

• the nucleotide sequence defining the sequence coordinates is not a RefSeqGene, LRG, or genomic RefSeq representing a chromosome or alternate locus.
• the format is valid HGVS but not the format preferred by NCBI.

HGVS, coding, RefSeq (c.)

The preferred HGVS expression on a RefSeq cDNA. ClinVar does not report all HGVS expressions for each version of a RefSeq cDNA or each splice variant. There is a selection for what is reported and displayed, namely

• a valid HGVS expression on the reference standard transcript defined by RefSeqGene, often calculated from a submission by ClinVar's automatic processing
• a valid HGVS expression on a cDNA from a submitter, even if the cDNA is not the reference standard transcript for RefSeqGene

HGVS, coding, LRG (c.)

A valid HGVS expression on the the coding transcript that is the reference standard transcript for the LRG.

HGVS, coding (c.)

A valid HGVS expression with the coding numbering system but not the reference standard transcript defined by either RefSeq or LRG. These cases usually include:

• the transcript is not a reference standard
• the report is gene-based
• the format is valid HGVS but not the format preferred by NCBI. For example,

HGVS, protein, RefSeq (p.)

The preferred HGVS expression on a protein, either:

• a valid HGVS expression on the reference standard protein defined RefSeqGene, often calculated from a submission by ClinVar's automatic processing.
• a valid HGVS expression on a RefSeq protein from a submitter, even if the protein is not the reference standard protein for RefSeqGene

HGVS, protein (p.)

A valid HGVS expression on a protein but not the preferred expression because:

• the protein is not a reference standard
• the format is valid HGVS but not the format preferred by NCBI.

HGVS, non-coding (n.)

The preferred HGVS expression for a non-coding transcript.

HGVS, RNA (r.)

The preferred HGVS expression for a reference RNA.

HGVS, uncertain

Used for all cases where there is ambiguity in defining the location of the variation.  These expressions are difficult to validate.

HGVS, non-validated

An HGVS expression on a nucleotide sequence that is not already treated as 'HGVS, uncertain' and that cannot be validated by NCBI. This may indicate that the HGVS expression is truly invalid, such as an incorrect location or reference nucleotide, OR that NCBI’s validation should be updated.

HGVS, previous

A valid HGVS expression, on any molecule type, on a previous version of an accession.