ClinVar Mutation representations and Descriptions

Question

[vigprasud]

I was looking into ClinVar data for getting mutation lists. There were mutations which were in the form GENE:c.*** representing they are CDS mutations and GENE:p.*** representing the amino acid changes.

What are those in the following forms represent?

1. m.***
2. GENE:n.***
3. GENE:g.***
4. nsv***

Example:

• TBC1D24:c.1143-6C>T - CDS mutation
• NP_002760.1:p.Cys139Ser - Protein mutation
• m.1606G>A - ??
• U43746.1:n.2241A>G - ??
• NC_000023.11:g.53254331_53296102dup41772 - ??
• nsv513787 - ??

[vigprasud]

Thanks that helped !

Answer 1

[Zhaorong]

They are the HGVS nomenclature.

The website is: http://www.hgvs.org/mutnomen/

But curiously, it is down right now.

Here is a cached copy.

Answer 2

[nilakshafreezon]

As per the readme.txt on ClinVar ftp download site.

variant_summary.txt
Generated monthly, the first Thursday of the month
A tab-delimited report based on each allele at a location on the genome for which data have been submitted to ClinVar.  


AlleleID                      integer value as stored in the AlleleID field in ClinVar  (//Measure/@ID in the XML)
Type                      character, the type of variation
Name                          character, the preferred name for the variation
GeneID                    integer, GeneID in NCBI's Gene database
GeneSymbol                character, comma-separated list of GeneIDs overlapping the variation
ClinicalSignificance      character, comma-separated list of values of clinical significance reported for this variation
RS# (dbSNP)               integer, rs# in dbSNP
nsv (dbVar)               character, the NSV identifier for the region in dbVar
RCVaccession              character, list of RCV accessions that report this variant
TestedInGTR            character, Y/N for Yes/No if there is a test registerd as specific to this variation in the NIH Genetic Testing Registry (GTR)
PhenotypeIDs              character, list of db names and identifers for phenotype(s) reported for this variant
Origin                    character, list of all allelic origins for this variation
Assembly                  character, name of the assembly on which locations are baed
Chromosome                character, chromosomal location
Start                     integer, starting location, in pter->qter orientation
Stop                      integer, end location, in pter->qter orientation
Cytogenetic            character, ISCN band
ReviewStatus          character, highest review status for reporting this measure
HGVS(c.)                  character, RefSeq cDNA-based HGVS expression
HGVS(p.)                  character, RefSeq protein-based HGVS expression
NumberSubmitters          integer, number of submissions with this variant
LastEvaluated             datetime, the latest time any submitter reported clinical significance
Guidelines                character, ACMG only right now, for the reporting of incidental variation in a Gene (NOTE: if ACMG, not a specific to the allele but to the Gene)
OtherIDs                      character, list of other identifiers or sources of information about this Gene