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List KnownVar

Command examples:

atav.sh --list-known-var --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-known-var: trigger list known var function.

--variant: use a variant id file (one id per line) or a variant id list (comma delimited).

id format: chr-pos-ref-alt

--known-var-only: use this option to restrict output variants only within ClinVar or HGMD variant set.

Output:

  • Variant ID: chr-pos-ref-alt
  • Gene Name: most damaging gene
  • HGMDm2site: Flags how many (and the details) of HGMD variants overlapping with a -2 position from the variant of interest. For multiple overlaps events separated with a pipe "|".
  • HGMDm1site: Flags how many (and the details) of HGMD variants overlapping with a -1 position from the variant of interest. For multiple overlaps events separated with a pipe "|".
  • HGMD site: Tally of how many variant-disease associations are reported in HGMD at the specific variant of interest site. Includes precise indel overlaps.
  • HGMD Disease: List of disease name(s) associated with the HGMD entry for this variant. Includes precise indel overlaps.
  • HGMD PMID: List of Pubmed ID for the publication(s) that resulted in the HGMD entries corresponding to the variant. Includes precise indel overlaps.
  • HGMD Class: List of HGMD classifications of variant (for more info see: http://www.hgmd.cf.ac.uk/ac/index.php). Includes precise indel overlaps.
  • HGMDp1site: Flags how many (and the details) of HGMD variants overlapping with a +1 position from the variant of interest. For multiple overlaps events separated with a pipe "|".
  • HGMDp2site: Flags how many (and the details) of HGMD variants overlapping with a +2 position from the variant of interest. For multiple overlaps events separated with a pipe "|".
  • HGMD indel 9bpflanks: For indels this highlights how many indels of any classification are reported in HGMD at the site and within 9bp flanking region.
  • ClinVar: Tally of how many variant-disease associations are reported in ClinVar at the specific variant of interest site.
  • ClinVar Disease: List of disease name(s) corresponding to the ClinVar "ConceptID"(s) assigned to the ClinVar variant.
  • ClinVar Clinical Significance: List of values of clinical significance reported for this variant (for more info see: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/README.txt).
  • ClinVar PMID: List of Pubmed ID for the publication(s) that resulted in the ClinVar entries corresponding to the variant.
  • ClinVar Other Ids: List of other identifiers or sources of information about this variant.
  • ClinVar pathogenic indels: This highlights how many "Pathogenic" indels are reported in Clinvar at the site and within 9bp flanking.
  • ClinVar all indels: This highlights how many indels of any classification are reported in Clinvar at the site and within 9bp flanking.
  • ClinVar Pathogenic Indel Count: indel "pathogenic/likely pathogenic" variants.
  • Clinvar Pathogenic CNV Count: CNV "pathogenic/likely pathogenic" variants.
  • ClinVar Pathogenic SNV Splice Count: Splice "pathogenic/likely pathogenic" variants.
  • ClinVar Pathogenic SNV Nonsense Count: Nonsense "pathogenic/likely pathogenic" variants.
  • ClinVar Pathogenic SNV Missense Count: Missense "pathogenic/likely pathogenic" variants.
  • ClinGen: Flags genes considered to be 'Halploinsufficient' by the ClinGen curation committee.
  • ClinGen HaploinsufficiencyDesc: ClinGen Dosage Sensitive Map (see: ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/clingen/ClinGen_gene_curation_list.tsv). Restricted to Haploinsufficiency curations.

"Unlikely" = Dosage sensitivity unlikely; "No evidence" = No evidence available; "Little evidence" = Little evidence for dosage pathogenicity; "Some evidence" = Some evidence for dosage pathogenicity; "Sufficient evidence" = Sufficient evidence for dosage pathogenicity; "Recessive evidence" = Gene associated with autosomal recessive phenotype.

  • ClinGen TriplosensitivityDesc: ClinGen Dosage Sensitive Map (see: ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/clingen/ClinGen_gene_curation_list.tsv). Restricted to Triplosensitivity curations.
  • OMIM Disease: List of OMIM disease associations linked to the Gene name linked to the variant (for more info see: http://www.omim.org/).
  • RecessiveCarrier: Curated indicator (1 = yes) of known Carrier disease genes as curated by IGM team members: Ayal Gussow and Matt Halvorsen March 2014.
  • ACMG: The annotation associated with a gene is three pieces of information separated by a pipe delimiter. All information is taken from Table 1 of Green et al.2013. First field = inheritance model | second field = Type of Variation to Report | third field = ACMG associated disorder.