Advanced Report Columns¶
Table view columns in the Variant listing of the Advanced report are broadly categorized by the following variant attribute categories:
These categories represent annotations derived from external databases, data quality scores calculated internally for the variant, study- and/or project-specific information, and reference information. Columns can be customized to show, hide, or order selected attributes (see Filtering Results).
Categories and columns are described in the tables below:
Default columns¶
Default columns display automatically when a tab is opened. These columns provide basic sequence variant call information, as well as clinically relevant annotations, links to external reference sources, and quality measures.
Category |
Column |
Description |
|---|---|---|
Default |
het or hom |
Heterozygous or homozygous variant at the designated position |
Sequence Variant |
Condensed summary description of the variant combining data from other columns including variant location, gene, reference variant, called variant, coding sequence and protein position, and associated disease information (see also Sequence Variant) |
|
CGD CONDITION |
Conditions resulting from variations in the same gene that may otherwise be placed in the “General” intervention category |
|
CGD INHERITANCE |
Patterns of inheritance, including:
|
|
VEP Max Impact |
The classification of the variant based on the severity of the consequence type on the transcript (“HIGH”, “MODERATE”, “LOW”, “LOWEST”); for a given variant, the maximum observed impact across the predicted transcripts from this position is reported (see also Variant Effect Predictor (VEP) Settings) |
|
VEP Max Consequence |
The consequence type reported for this variant that has the greatest biological impact; for a given variant, the maximum observed consequence across the predicted transcripts from this position is reported (see also Variant Effect Predictor (VEP) Settings) |
|
VEP Max Af |
Maximum reported population allele frequency derived from the 1000 Genomes Project phase 3 (1000G3), Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genomes of the Netherlands (GONL), and Kyoto population surveys (see also popAlleleFreq) |
|
VEP Max Score |
Maximum score for the variant as observed in dbNSFP (Score=max of (1-Sift_score), Polyphen2_HDIV_score, or Polyphen2_HVAR_score) |
|
Gene cov |
Fraction of genes (exome) with depths of less than 5 (red), ranging from 5-9 (orange), and greater than 9 (green); note that the scale ranges from 0 to 50% to make the red/orange bars longer, emphasizing low coverages |
|
GT CallRatio |
Proportion of reads containing the variant call (expect a value of approximately 0.5 for heterozygous calls and approximately 1 for homozygous calls) |
|
GT Depth |
Number of reads used for evaluating the corresponding call |
|
KNOWN Gene diseases |
Diseases known to be associated with variants in the gene, as annotated by ClinVar, HGMD, and OMIM |
|
Known pmid |
Pubmed ID of the reference from which the information was obtained |
|
KNOWN var diseases |
Diseases known to be associated with the variant as annotated by ClinVar, HGMD, and OMIM |
|
OMIM IDs |
Online Mendelian Inheritance in Man (OMIM) IDs |
|
rsIDs |
Reference SNP identifiers assigned by NCBI to a group of SNPs that map to an identical location |
Diagnostic (DIAG) columns¶
DIAG columns provide diagnositic information for categorizing variants in a clinical setting, based on American College of Medical Genetics and Genomics (ACMG) guidelines. Note that “diagnosis” is abbreviated as “dx” in some cases.
Category |
Column |
Description |
|---|---|---|
Diagnostic (DIAG) |
HomRecess |
“Homozygous recessive variant” is reported when both alleles present at the genomic position are identical and none of the controls are homozygous at that position |
CHZ |
Compound heterozygous (CHZ) variant (see GENE_CHZinGene) where none of the controls (including parents if non-affected) are homozygous and the cases might also potentially be CHZ. Analysis of the index case takes into account the variant phase if the parents are also provided; however, if the parents are not provided, the phase of the variants is assumed to be different. Compound heterozygosity in the same gene in controls does not prevent DIAG_CHZ from being true because without phased variants, the CHZ status is very sensitive (i.e., only two variants in the gene are required). Below is an example how DIAG_CHZ is calculated when both parents are unaffected:
The variables CaseDelta and CtrlDelta can be used to relax the condition, i.e., how many of the cases match and how many of the controls are in disagreement with the observations in the index case. |
|
Dominant |
This field is “true” if the variant is not present in unaffected individuals but is present in affected individuals; for example, with unaffected parents, dominance is calculated as follows:
The variables CaseDelta and CtrlDelta can be used to relax the condition, i.e., how many of the cases match and how many of the controls are in disagreement with the observations in the index case. In cases in which there are no additional affected individuals (cases), novel variants classified as dominant. |
|
recessiveCat |
Recessive and compound heterozygosity, based on the ACMG category for two alleles from any two variants observed in a gene, or from a homozygous variant. For an allele combination in the index case to be considered a potential recessive or compound heterozygous candidate, it may not be present in any of the controls (unless ctrlDelta is greater than zero). If the alleles in the index can be phased, they are considered only if they are not known to be from the same parent. In controls, the phase of alleles is assumed to be different (see recessiveCat) |
|
otherPos |
The base pair position of other variants that form compound heterozygosity with a variant |
|
otherACMGcat |
The ACMG category of other variants (see DIAG_otherPos and DIAG_compPhases) that form compound heterozygosity with the variant |
|
model |
Each variant that lies in chromosomes 1-22 is analyzed as “Autosomal”; variants on the X chromosome are analyzed as “X-linked” |
|
rank recessive |
An empirical ranking of variants; low-ranking variants should be better candidates for recessive variants than those with a high ranking; ranking takes into consideration homozygosity and compound heterozygosity in the affected vs. unaffected individuals; the smaller the DIAG_recessiveCat value (e.g., ‘1:DxConsistent’, ‘2:DxLikely’, ‘3:DxPossible’, etc.), the larger the weight of the variant |
|
rank dominant |
An empirical ranking of variants; low-ranking variants should be better candidates for dominant variants than those with a high ranking; ranking takes into consideration how many affected individuals share the same variant or any variants in the same gene, and how few controls have the variant or any variant in the same gene (see also DIAG_Dominant) |
|
deNovo |
A Boolean column indicating whether a variant is de novo (i.e., not present in the parents) |
|
compPhases |
The phase of the variant and the other variant in the gene (see DIAG_otherPOS and DIAG_otherACMGcat); used when the index case is analyzed for compound heterzygosity Example values include:
All variants within a gene are filtered according to the following condition: where hetORhom = ‘hom’ and pos = posx or pos != posx and (GT_phasex = ‘F/M’ or GT_Phasex = ‘U’ or GT_Phase != GT_Phasex)
Here pos represents the position of the first variant, and posx represents the position of the second variant. Likewise for GT_Phase and GT_Phasex. |
Clinical Genomic Database (CGD) columns¶
CGD columns provide information that is based on the manually curated database of variants associated with known medically significant conditions and available interventions. For more information, visit https://research.nhgri.nih.gov/CGD/.
Category |
Column |
Description |
|---|---|---|
Clinical Genomic Database (CGD) |
AGE GROUP |
Pediatric: less than 18 years of age; Adult: at least 18 years of age |
COMMENTS |
Conditions also resulting from mutations in the same gene but may otherwise be placed in the “General” intervention category |
|
INHERITANCE |
The pattern of inheritance the variant is known to follow:
|
|
INTERVENTION CATEG or IES |
Includes organ systems for which specific and additional inteventions may be beneficial |
|
INTERVENTION RATIONALE |
A description of the intervention and its benefit |
|
MANIFESTATION CATEG or IES |
Includes organ systems affected by mutations in corresponding genes; recognition of involved organ systems may help guide supportive care |
Variant Effect Predictor (VEP) columns¶
VEP columns provide functional annotation for variants based on the Ensembl SNP Effect Predictor database. For more information, visit http://www.ensembl.org/info/docs/tools/vep/index.html.
Category |
Column |
Description |
|---|---|---|
Variant Effect Predictor (VEP) |
Max Impact |
The classification of the variant based on the severity of the consequence type on the transcript (“HIGH”, “MODERATE”, “LOW”, “LOWEST”); for a given variant, the maximum observed impact across the predicted transcripts from this position is reported (see also Variant Effect Predictor (VEP) Settings) |
Max consequence |
The consequence type reported for this variant that has the greatest biological impact; for a given variant, the maximum observed consequence across the predicted transcripts from this position is reported (see also Variant Effect Predictor (VEP) Settings) |
|
Max Af |
The maximum reported population allele frequency, derived from the 1000 Genomes Project phase 3 (1000G3), Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genomes of the Netherlands (GONL), and Kyoto population surveys (see also popAlleleFreq) |
|
Consequence |
Annotation of the consequence type in the canonical transcript of the annotated variant |
|
Max Score |
The maximum score for the variant, as observed in dbNSFP (Score=max of (1-Sift_score), Polyphen2_HDIV_score, or Polyphen2_HVAR_score) |
|
Amino Acids |
Protein sequence change(s) provided for variants affecting the protein-coding sequence; a value is given for each transcipt |
|
Protein Position |
The position of the amino acid in the protein sequence (only if the variant falls within a coding sequence); a value is given for each corresponding transcipt specified in the CDS position column |
|
Refgene |
Accession number from NCBI for the Refseq transcript using lookup into Ensembl 73 using feature |
|
CDS position |
The position of the base pair in the coding sequence; a value is given for each transcript |
|
Transcript count |
The number of different transcripts in which the variant is found |
Gene columns¶
Gene columns provide information based on the candidate gene in which a variant is found. Where possible, the HUGO Gene Nomenclature Committee (HGNC) gene symbol is provided (for more information, visit https://www.genenames.org).
Category |
Column |
Description |
|---|---|---|
Gene |
symbol |
The gene identified by viewing the variant in Ensembl; output is the HGNC gene symbol for the identified gene (clone name provided when HGNC symbol is unavailable) |
Aliases |
Gene aliases, including the main symbol |
|
avg depth |
The average sequence read depth in the exome for a given gene |
|
candidate paralogs |
Paralogs of a gene that is included in the Candidate genes list |
|
candidate Phenotypes |
Phenotypes and gene lists that match the variant gene as a paralog (orange) or a candidate gene (green) |
|
cand or paralog |
Value is “c” if the gene is a candidate gene and “p” if it is a paralog of one of the candidate genes |
|
Cand PhenoScore |
The phenotype significance score over candidate genes |
|
DmaxAf |
The maximum allowed allele frequency for a dominant variant |
|
exomeSize |
The sum of the base pair size of all of the exons in the gene |
|
exontype |
Coding or non-coding region |
|
homozVarsInGene |
The number of homozygous variants the index case has in a given gene |
|
knownVarsInGene |
The number of known (e.g., in HGMD) variants the index case has in a given gene |
|
lt10 |
Fraction of the exome with sequence read coverage less than 10 |
|
lt15 |
Fraction of the exome with sequence read coverage less than 15 |
|
lt20 |
Fraction of the exome with sequence read coverage less than 20 |
|
lt25 |
Fraction of the exome with sequence read coverage less than 25 |
|
lt30 |
Fraction of the exome with sequence read coverage less than 30 |
|
lt5 |
Fraction of the exome with sequence read coverage less than 5 |
|
MOI |
Mode of inheritance determined for the gene based on the alleles present |
|
Paralogs |
The paralog (gene duplication) of a given gene |
|
RmaxAf |
The maximum allowed allele frequency for a recessive variant |
|
RmaxGf |
The maximum allowed genotype frequency for a compound heterozygous variant |
|
varsInGene |
The total number of variants in a gene for the index case |
|
cov |
Fraction of genes (exome) with depths of less than 5 (red), ranging from 5-9 (orange), and greater than 9 (green), scaled from 0 to 50% of the actual coverage to emphasize lower-coverage regions (red/orange) |
CASEs columns¶
CASEs columns provide variant counts for affected individuals in a project.
Category |
Column |
Description |
|---|---|---|
CASEs |
homozVarsInGene |
Equal to 1 if subjects in the affected case group have a homozygous variant in the given gene |
knownVarsInGene |
The number of known variants (e.g., those listed in HGMD) that the affected case group has in a given gene |
|
subjCompHeterInGene |
Equal to 1 if the affected case group is potentially compound heterozygous for a given gene, otherwise it is equal to 0; based on a loose definition for compound heterozygosity, i.e., it requires only the case to have a single homozygous variant or two heterozygous variants in a given gene |
|
subjWithVarInGene |
Equal to 1 if the affected case group has a variant in the given gene, otherwise it is equal to 0 |
|
withHomoVar |
Equal to 1 if the affected case group is homozygous for a given variant |
|
withVar |
Equal to 1 if the affected case group has the variant, otherwise it is equal to 0 |
Comments (COMM) columns¶
COMM columns provide variant annotations that have been added by users in the project.
Category |
Column |
Description |
|---|---|---|
Comments (COMM) |
Approval months |
Counter for months since the date of last approved clinical significance |
Approved clinical significance |
The approved clinical significance by the user |
|
BAM confirmed |
User confirmation that the BAM file was reviewed to confirm the presence of the variant |
|
Clinical Significance |
The clinical significance of the variant as annotated (commented) by users (e.g., pathogenic, benign, unknown significance, drug-response, risk factor, etc.) |
|
Created at |
The date and time that the comment was created |
|
Disease |
User-added disease with which the variant is associated |
|
Gene symbol |
The gene symbol from the varcomments table |
|
HGVScp |
User-added Human Genome Variant Society (HGVS), transcript, cDNA nomenclature, and protein nomenclature; can be populated by automatically selecting a transcript in the COMM_transcript_raw column and editing the field as needed |
|
ID |
Comment ID |
|
Internal comment |
User-added internal comment on a variant |
|
Interpretation |
User-added interpretation of a variant |
|
Is active |
Boolean value: 1=active |
|
Last approved at |
The date that the variant was last approved |
|
Mode of inheritance |
User-annotated (commented) mode of inheritance of the variant |
|
Onset |
User-curated onset of the disease with which the variant is associated |
|
Orthogonal sequencing status |
User-added orthogonal sequencing confirmation status |
|
OTHER active annotations |
Annotations on this variant exist in a separate study |
|
OTHER allele |
User-added other allele with which this variant is in compound |
|
OTHER clinical significance |
Clinical significance of the variant available from another study |
|
OTHER interpretation |
Interpretation of the variant available from another study |
|
OTHER last approved at |
The date of the last approved and current status of a variant available from another study |
|
OTHER variant review status |
Variant review status of a variant available from another study |
|
Owner |
The user who entered the curation |
|
Parental origin |
User-selected parental origin of the variant (e.g., father, mother, both, de novo, unknown, etc.) |
|
PN |
Patient number |
|
Reported at |
The date of the variant annotation |
|
Reporting category |
User-selected category, related to client workflow |
|
Report section |
User-selected report section where the selected variant should be placed |
|
Report status |
Related to client workflow to indicate what to report |
|
Report type |
Related to client workflow to indicate the type of report |
|
Severity |
User-added severity of the disease with which the variant is associated |
|
Starred |
Indicates whether the variant has been starred (flagged) by a user |
|
Text |
The description (comment) component for the user’s annotation of the variant |
|
Transcript raw |
All possible transcripts with HGVS nomenclature for the variant for user to select. |
|
User id |
Internal CSA Web user ID |
|
Variant review status |
User-added variant review status |
EuroGeneTest columns¶
EuroGenetest columns are derived from a European Commission project database that contains European genetic testing information for particular genes, variants, and diseases. For more information, visit http://www.eurogentest.org/index.php?id=160.
Category |
Column |
Description |
|---|---|---|
EuroGenetest |
Diseases |
Diseases associated with a variant |
EuroGenetest NoOfDiseases |
The number of diseases associated with a variant |
|
EuroGenetest NoOfpanels |
The number of gene panels associated with a variant |
|
EuroGenetest panels |
EuroGentest gene panels associated with a variant |
Gene Ontology (GO) columns¶
GO columns provide a functional annotation of the gene product in which the variant is found. For more information, visit http://geneontology.org.
Category |
Column |
Description |
|---|---|---|
Gene Ontology (GO) |
Descriptions |
Gene ontology category descriptions |
IDs |
Gene ontology identifier codes |
Geneotype (GT) columns¶
GT columns provide quality control information for the variant call, based on the sequence read depth and quality. These scores are based on the Genome Analysis Toolkit (GATK) measures.
Category |
Column |
Description |
|---|---|---|
Genotype (GT) |
CallCopies |
Variations from the reference are reported by default; CallCopies refers to how many copies of the variation exist in a subject; a CallCopies value of “2” therefore corresponds to a homozygous variant, whereas a CallCopies value of “1” corresponds to a heterozygous variation |
CallRatio |
Proportion of reads containing the variant call; this number is expected to be close to 0.5 for heterozygous calls and close to 1 for homozygous calls |
|
Depth |
The number of reads used for evaluating the corresponding call |
|
FILTER |
Quality parameter that uses the ratio between the genotype quality and depth, showing whether the call is considered “LowQual” quality (not useable) or “PASS”; this remains a crude quality measure |
|
GL Call |
A statistical measure indicating the likelihood that a call is wrong; the scale has been converted to using only integers - the higher the number, the less likely that the call is wrong |
|
IHEstatus |
Inheritance error status (1 = error, 0 = ok) |
Known columns¶
Known columns provide publicly available information about the candidate gene and/or variant based on annotations listed in the HGMD, ClinVar, and OMIM databases.
Category |
Column |
Description |
|---|---|---|
Known |
ClinVarAcc |
ClinVar accession(s) |
distance |
The distance between a known variant and the identified variant |
|
GeneLists |
The gene list where the gene in which the variant is found is a member |
|
Gene diseases |
Diseases known to be associated with variants in the gene |
|
Gene par diseases |
Diseases known to be associated with the paralog genes of the given gene |
|
HGMDacc |
The HGMD accession of the known variant |
|
InACMG |
A Boolean column (1/0) indicating whether the gene is in the ACMG recommended list for incidental findings |
|
PMID |
Pubmed ID of the reference from which the information was obtained |
|
Refgene |
mRNA accession number from NCBI using lookup into Ensembl using feature |
|
Source |
Source database of the known variant |
|
var diseases |
Diseases known to be associated with the variant |
|
variantType |
Variant type in the source database. For HGMD:
|
|
varType |
The type of variant: “sub” (substitution), “del” (deletion), “ins” (insertion), “indel”, etc. |
|
Variant review status |
The currently selected variant review status value from the variant annotation |
Online Mendelian Inheritance in Man (OMIM) columns¶
OMIM columns provide the OMIM-designated identification for a particular gene and related disease description. For more information, visit https://www.ncbi.nlm.nih.gov/omim.
Category |
Column |
Description |
|---|---|---|
OMIM |
Descriptions |
OMIM disease descriptions for the gene |
IDs |
OMIM IDs |
MOTHER/FATHER columns¶
MOTHER/FATHER columns provide the variant information of the parents in a project.
Category |
Column |
Description |
|---|---|---|
MOTHER/FATHER |
apprCovDepth |
Read depth for the mother/father in the location of the variant |
Call |
The variant call of the mother/father; if the mother/father does not have the allele of the index variant, the value is “Var_Absent” |
|
het or hom |
“hom” for homozygosity, “het” for heterozygosity, or “NA” if the value in the Call column is “Var_absent” |
|
homozVarsInGene |
Equal to 1 if the mother/father has a homozygous variant in the given gene |
|
knownVarsInGene |
The number of known variants (e.g., in HGMD) the mother/father has in the given gene |
|
readsWithVar |
Number of reads that carry the variant in the mother/father in the location of the variant |
|
subjCompHeterInGene |
Equal to 1 if the mother/father is potentially compound heterozygous in the given gene, otherwise 0; based on a loose definition of compound heterozygosity, i.e., it requires only the case to have a single homozygous variant or two heterozygous variants in the given gene |
|
subjWithVarInGene |
Equal to 1 if the mother/father has the variant in the given gene, otherwise 0 |
|
withHomoVar |
Equal to 1 if the mother/father is homozygous for the given variant, otherwise 0 |
|
withVar |
Equal to 1 if the mother/father has the variant, otherwise 0 |
Other columns¶
Other columns provide information not included in the previously described categories.
Category |
Column |
Description |
|---|---|---|
Other |
Chrom |
Variant chromosome location |
Pos |
Nucleotide from the reference build at the base pair position in the Pos column |
|
Call |
Sequence (variant) called based on the reference sequence at the designated position |
|
ID |
Reference SNP identifiers assigned by NCBI to a group of SNPs that map to an identical location |
|
CLNACC |
ClinVar assigned variant accessions and versions |
|
PN |
Patient number (identifier) |
|
Carrier |
A Boolean column (1/0) indicating if the individual carries the variant |
|
FS |
Fisher’s exact test of read strand; if the reference reads are balanced between forward and reverse strands, then the alternate reads should be as well |
|
formatZip |
VCF genotype fields |
|
HGVSc |
The HGVS coding sequence name |
|
HGVSp |
The HGVS protein sequence name |
|
Biotype |
Additional annotation using Ensembl lookup based on feature (e.g., miRNA_PUTATIVE, misc_RNA_PUTATIVE, protein_coding_PUTATIVE, pseudogene_PUTATIVE, snoRNA_PUTATIVE) |
|
CHROMO |
The chromosome of the variant represented as chr1, chr2, …, chr22, chrX, chrY, or chrM |
|
POSx |
The base pair position of a known variant within the same codon of the identified variant |
|
Source |
For trio cases, the participant in the study sharing the same variant |
|
Sourcex |
For trio cases, additional participants in the study sharing the same variant |
|
comment |
User-entered comments for the variant |
|
starred |
A Boolean column (1/0) indicating if the variant has been starred (flagged) for inclusion in the generated report |