Profile Settings

The Profile settings page may contain the following tabs:

• Account settings - personal settings, including email address, login, and password, as well as preferences for the application navigation panel, the patient page, SNV Viewer, and CNV Viewer.
• Payments - information about completed and upcoming payments for using Genomenal. This tab is available only if billing is enabled for the user (configured by an administrator).
• Usage Details - information about the user's Genomenal product usage and the calculated cost for the selected period. This tab is available only if billing is enabled for the user (configured by an administrator).
• Pricing - the current prices for Genomenal products. This tab is available only if billing is enabled for the user (configured by an administrator).
• Statistics/Export - statistics for interpreted SNVs/Indels and the ability to export them.

To open "Profile settings" page, hover over your username at the bottom of the navigation panel and click on the three
dots . In the opened menu, select "Profile":

You will see a settings page:

Account settings

Email address

Здесь вы можете посмотреть, какой email вы использовали при регистрации в Системе. Для того чтобы его поменять, нажмите на , а затем в открывшемся окне введите новый адрес почты и ваш действующий пароль аккаунта для подтверждения действия:

Here you can see what email you used when registering in the System. In order to change it, click on , and then in the window that opens, enter a new email address and your current account password to confirm the action:

After filling out the form, click on . Now check the inbox of the email that you indicated as new, and confirm the change of address in the letter.

Login

Here you can see which login you used when registering in the System. In order to change it, click on , and then in the window that opens, enter a new login and your current account password to confirm the action:

After filling out the form, click on . Login successfully changed!

Login can consist of any characters up to 128.

Password

To change the password for logging into the System, click on , and then in the window that opens, enter your current account password to confirm the action and enter the new password twice:

After filling out the form, click on . Password successfully changed!

Password can consist of any characters up to 128.

Program Language

Here you can choose the Program language that is more convenient for you. To do this, click on the language selection field and select the language in the drop-down list:

Notification about processing completion

Here you can configure receiving notifications when sample processing and group analyzes are complete. Sample analysis completion notifications are sent when all samples uploaded into a single patient or run have completed processing. When you restart processing a sample or group analysis, you will also receive a completion notification. Notifications are sent to the email chosen in your account settings. In the email, you will find a link to the page of the patient or run whose sample processing has completed, or a link to the completed group analysis. For patients and runs, links to samples whose processing completed successfully or with failures will be provided. To receive notifications when sample processing or group analyzes are completed, enable the corresponding option "Notify when processing is finished".

Navigation panel

The section displays which page sections are shown on the Program navigation panel in addition to the home page "Samples" (all are selected by default):

To remove a section from the panel, uncheck it.

Patient page

There can be two tabs on the patient page: "Main" and "CNV Report" if "CNV Report" has been generated (see conditions here):

In this section, you can configure which tab you will see first when you open the patient page:

• the "Main" tab, which contains information about the patient and uploaded sample sets (chosen by default);
• the "CNV Report" tab with a report on the results of the copy number analysis in the patient samples.

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If the patient "CNV Report" has not been generated at all or is still being generated, then even if you have selected the "CNV Report" tab here, the "Main" tab will open.

SNV Viewer

SNV Viewer is an embedded service for viewing and analyzing variants. It is described in detail in the corresponding section.

Filtering mode

SNV Viewer has two variant filtering modes: Basic with basic filters and Advanced with more filters and the ability to compose complex queries with multiple filter conditions.

In this section, you can configure which filtering mode you will see when you first open the sample SNV Viewer page (Basic Filtering chosen by default):

Filters in Basic Filtering mode

The default filters are described here:

You can change the choice of filters (remove or add new ones):

Available filters:

• Samples is a filter of variants by run samples in which these variants were discovered. Displayed only in the run SNV Viewer. Added by default.
• Samples Type is a filter of variants by the type of run samples in which these variants were discovered: normal only or tumor only. Displayed only in the SNV Viewer of runs that contain both normal and tumor samples.
• Sample Interpretation Status is a filter of variants by the interpretation status of the run sample in which these variants were discovered (completed or uncompleted interpretation). Displayed only in the run SNV Viewer.
• Origin is a variant filter by mutation type: Somatic or Germline. Added by default. Not displayed in SNV Viewer with germline mutations and the group analysis SNV Viewer.
• Gene panel is a variant filter by gene panel. Added by default.
• Gene is a variant filter by gene transcripts in which variants are located. Added by default.
• Ontology is a variant filter by their localization in genes associated with terms from the Human Phenotype Ontology (HPO) and the Mondo Disease Ontology (Mondo). Added by default.
• Pathogenicity is a variant filter by pathogenicity determined manually by the user, by ACMG criteria or by pathogenicity database: Pathogenic, Likely pathogenic, Uncertain significance conflict (conflicting interpretations of pathogenicity), Uncertain significance, Likely benign, Benign, Undefined.
• Label is a variant filter by significance defined by the user: High significance, Moderate significance, Low significance, Sequencing error, Undefined.
• ClinVar is a variant filter by the clinical significance of the phenotype according to ClinVar database (you can find the description of values here).
• Consequence is a variant filter by effects on genes. The values are described here.
• Caller Filters is a variant filter by GATK variant filters.
• Min Depth level is a variant filtering scale by the minimum level of sequencing depth. Added by default.

• Trio GT is a variant filter by inheritance: De novo variants, Newly formed homozygotes (homozygotes in proband that are heterozygous in parents) or Single parent-inherited. Added by default, available only in Family group analysis for Trio case (Proband, Father and Mother).
• gnomAD 3 AF is a variant filter by allele frequency (AF) in gnomAD 3 database:

• <0.05 (threshold between common and rare variants) or empty (no allele frequency data in gnomAD);
• <0.02 (conditional threshold of a hypomorph) or empty;
• <0.01 (estimated threshold of autosomal recessive inheritance) or empty;
• <0.005 (estimated threshold of X-linked inheritance) or empty;
• <0.0001 (estimated threshold of autosomal dominant inheritance) or empty.

• Region - filter variants by the position on genome (chromosome, start and end positions).

Preferred gene transcript model

On "Gene" tab of the variant details panel, gene transcripts from two databases are available: Ensembl and RefSeq. By default, a table with transcripts from Ensembl is shown.

In this section, you can configure which gene transcript model will be shown by default:

Advanced filtering conditions

In advanced filtering mode, the query conditions for the searched variants are displayed at the top of the SNV Viewer table. When there are a lot of conditions in a query, it is convenient to collapse them so that they do not take up much space on the page.

In this section, you can configure whether the query conditions will be expanded (by default) or collapsed immediately after applying the filtering query:

SNV & CNV Viewer

SNV Viewer is an embedded service for viewing and analyzing variants. It is described in detail in the corresponding section.
CNV Viewer is an embedded service for viewing and analyzing copy number variations (CNVs).

Variant details bottom panel

The variant detailed information panel contains main information about the selected variant. By default, it is expanded at the bottom of the SNV or CNV Viewer table. If you don't usually use the panel, you can hide it from SNV and CNV Viewers by selecting the "Collapse" option:

Return to default settings

If you have made changes to the language selection, navigation bar, patient page, SNV Viewer, or CNV Viewer settings, you can return to the default settings by clicking on . Please note that the action will immediately reset all changes that you made on the page (except for changes to email, login and password).

Payments

The Payments tab is available only if billing is enabled for your account (configured by an administrator). The page displays information about your completed and upcoming payments for using Genomenal.

At the top of the tab, the amount due (in RUB) as of the beginning of the current month is displayed. This amount is updated automatically as information about received payments is added.

Completed payments are displayed in a table with the following columns:

• Payment amount - the payment amount in RUB;
• Payment date - the date the payment was made;
• Comments - additional information about the payment.

Usage Details

The Usage Details tab is available only if billing is enabled for your account (configured by an administrator). The page displays information about your usage of Genomenal products and the calculated cost for the selected time period.

At the top of the tab, you can select the time period for which usage details are displayed. By default, the period spans from the first day of the current month to the current date.

Usage details for the selected period are presented in a table with the following columns:

1. Product - the name of the service provided. Expanding a row displays the samples or group analyses for which the service was provided.

The expanded entries are displayed in the following formats:

• Patient samples: patient ID / sample name
• Run samples: run name / sample name
• Patient samples in a run: run name / patient ID / sample name
• Group analyses: group analysis name (Samples: number of samples included in the analysis)

The names link to the corresponding pages.
If a sample has been deleted after processing, its name is displayed without a link and is followed by the label (deleted).

2. Usage - represents the amount of resources consumed or the number of services provided during the selected period.

• For Processing, Annotation, and Group analysis services, the value represents the number of completed operations.
• For the Analysis support service, the value represents the total size of stored sample files, expressed in GB*day (1 GB of data stored for 1 day).
• For the SNV viewer support service, the value represents the total number of stored genetic variants (SNVs/Indels), expressed in 100K SNV*day (100,000 variants stored for 1 day). The displayed value is rounded.

Actual usage is calculated as: Usage − Added. The added amount is excluded from billing because storage is provided free of charge for the first 30 days after sample processing.

For Processing, Annotation, and Group analysis services, detailed usage information is available in the expanded rows.

3. Cost - the cost of the service for the selected period (in RUB).

The general formula is: Cost = Actual Usage × Unit Price / 30 days

Prices are available on the Pricing tab.

• The cost of Processing, Annotation, and Group analysis services depends on the number of processed samples or completed group analyses during the selected period.
• The cost of Analysis support depends on the total size of the stored sample files.
• The cost of SNV viewer support depends on the number of stored SNVs/Indels.

For Processing, Annotation, and Group analysis services, detailed cost information is available in the expanded rows.

The bottom row of the table (Total for the period) displays the total cost of all services during the selected period.

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To reduce the cost of Analysis support and SNV viewer support, you can compress a sample by deleting the FASTQ files and SNV Viewer data, respectively.

4. Details - contains additional information for each service.

Details for Processing, Annotation, and Group analysis:

• Processed at – the date and time when the sample or group analysis was processed.

Details for Analysis support:

• GB*day on period start - the storage usage carried over to the beginning of the selected period. This value is always 0, because each reporting period is calculated independently and accumulated usage is not carried over.
• GB*day added for the period - the amount of newly stored data during the selected period that is excluded from billing. This value is recalculated for the full 30-day free storage period according to the formula: Storage Size (GB) × 30 days.
• GB*day used for the period - the actual storage usage during the selected period, calculated as: Storage Size (GB) × Actual Storage Time (days).
• GB*day on period end - the storage usage at the end of the selected period. This value is always 0, because each reporting period is calculated independently. **Expanded row details for Analysis support:**
• Sample files size - the size of a single sample file, or the combined size of the primary and mate files for paired-end sequencing.
• Period - the time interval selected at the top of the Usage Details tab. Usage is calculated in whole days within the selected period according to the System time zone.
• GB*day added for the period - see above.
• GB*day used for the period - see above.

Details for SNV viewer support:

• 100K SNV*day on period start - the number of SNVs/Indels counted at the beginning of the selected period. Always 0, because each reporting period is calculated independently.
• 100K SNV*day added for the period - the number of SNVs/Indels added during the selected period and excluded from billing. This value is recalculated for the full 30-day free storage period according to the formula: Stored Variants (100K SNV) × 30 days.
• 100K SNV*day used for the period - the actual usage during the selected period, calculated as: Stored Variants (100K SNV) × Actual Storage Time (days).
• 100K SNV*day on period end - the number of SNVs/Indels counted at the end of the selected period. Always 0, because each reporting period is calculated independently.

Expanded row details for SNV viewer support:

• SNV count for sample - the total number of variants stored in the sample's SNV Viewer. If both somatic and germline variants are present, their counts are added together.
• Period - the time interval selected at the top of the Usage Details tab. Usage is calculated in whole days within the selected period according to the System time zone.
• 100K SNV*day added for the period - see above.
• 100K SNV*day used for the period - see above.

Total for the period row at the bottom of the table displays:

• Debt on period start - the unpaid balance at the beginning of the selected period (RUB).
• Period payments - the total amount of payments received during the selected period (RUB).
• Cost of usage for the period - the total cost of all services during the selected period (RUB).
• Debt on period end - the amount due for the selected period (RUB), calculated as: (Debt on period start) + (Cost of usage for the period) − (Period payments).

Pricing

The Pricing tab is available only if billing is enabled for your account (configured by an administrator). The page displays displays the current prices for Genomenal products.

The prices are displayed in a table with the following columns:

1. Product - the name of the Genomenal service:

• FASTQ/BAM gene panel processing;
• FASTQ/BAM whole-exome processing;
• FASTQ/BAM whole-genome processing;
• FASTQ/BAM low-pass whole-genome processing;
• VCF gene panel annotation;
• VCF whole-exome annotation;
• VCF whole-genome annotation;
• VCF Structural variations annotation;
• Analysis support, 1GB per 30 days (the first 30 days after sample processing are free of charge);
• Group analysis of FASTQ/BAM gene panels, per sample (price depends on the number of samples in the analysis);
• Group analysis of FASTQ/BAM whole-exome samples, per sample (price depends on the number of samples in the analysis);
• Group analysis of FASTQ/BAM whole-genome samples, per sample (price depends on the number of samples in the analysis);
• SNV viewer support, 100000 variants per 30 days (the first 30 days after sample processing are free of charge).

2. Price - the price of the product (in RUB). A personal price is indicated by the icon.
3. Valid from - the date from which the price becomes effective.

Statistics/Export

The page provides statistics for interpreted SNVs/Indels and allows you to export this data.

The statistics include data for both existing and deleted patients, runs, and group analyses in which SNVs/Indels were discovered.

Only SNVs/Indels that meet at least one of the following criteria are included:

• a pathogenicity has been determined;
• a variant interpretation has been added;
• the variant has been pinned in SNV Viewer.

The table displays the following statistics for interpreted SNVs/Indels:

• Patients - the number of patients whose samples contain interpreted SNVs/Indels.
• Samples - the number of samples containing interpreted SNVs/Indels.
• Runs - the number of runs containing samples with interpreted SNVs/Indels.
• Group analyses - the number of group analyses containing interpreted SNVs/Indels.
• Records - the total number of interpreted SNVs/Indels.

To export the interpreted SNVs/Indels as a CSV file, click .

The exported table contains the following columns:

• type – the record type:

  • Sample SNV – a variant discovered in a sample;
  • Group Analysis SNV – a variant discovered in a group analysis;
  • Group Analysis Sample – a sample belonging to a group analysis in which the variant was discovered.

• Patient information: fields describing the patient to whom the sample containing the variant belongs. These fields generally correspond to those in the "Patient Info" section:

  • patients.patientId - patient ID;
  • patients.firstName - first name;
  • patients.lastName - last name;
  • patients.middleName - middle name;
  • patients.sex - sex;
  • patients.diagnosis - provided diagnosis;
  • patients.description - comments;
  • patients.dateOfDiagnosis - date of diagnosis;
  • patients.dateOfBirth - date of birth;
  • patients.archived - whether the patient's data is archived: true or false;
  • patients.inProgress - whether the patient's data is currently being processed: true or false;
  • patients.problems - whether any processing issues or quality concerns have been identified for the patient's data: true or false;
  • patients.readOnly - whether the patient's data is read-only: true or false;
  • patients.deleted - whether the patient's data has been deleted: true or false.

• Run information: fields describing the run to whom the sample containing the variant belongs:

  • runs.name - run name;
  • runs.description - description;
  • runs.sampleType - samples type in run;
  • runs.archived - whether the run is archived: true or false;
  • runs.deleted - whether the run has been deleted by the user: true or false;
  • runs.deletionFinalized - whether the run deletion process has been completed: true or false;
  • runs.virtual - whether the sample in the run is a demo sample: true or false.

• Sample information: fields describing the sample that contains the variant. These fields generally correspond to those in the "Sample Info" section:

  • sample_sets.name - file name. Populated only if the sample is added to a run but is not assigned to any patient.
  • sample_sets.status - sample processing status: SUCCESS, IN_PROGRESS, FAILED;
  • sample_sets.problems - whether any processing issues have been identified during the sample processing: true or false;
  • source_files.name - file name;
  • source_files.description - comments;
  • source_files.sourceType - uploading source type:
    • FILE - file;
    • SRA - run code from NCBI SRA;
    • URL - link to the file on the FTP, HTTP servers, Yandex.Disk, or Google Drive.
  • source_files.source - file source. Depending on the value of the source_files.sourceType field, it contains the file name, the NCBI SRA run code, or a link to the file;
  • source_files.alias - alias;
  • source_files.sampleType - sample type: NORMAL or TUMOR;
  • source_files.format - file format: FASTQ_GZ or VCF;
  • source_files.formatFeature - format feature;
  • source_files.readsType - reads type: DNA, RNA, UNKNOWN;
  • source_files.sequencer - sequencer: ILLUMINA, ION_TORRENT, BGI, UNKNOWN;
  • source_files.sequencingType - sequencing type: PANEL, WES, WGS, LOW_PASS_WGS, UNKNOWN;
  • source_files.fileSize - file size in bytes (B);
  • source_files.sampleLocation - sample location (organ);
  • source_files.sampleCollectionDate - sample collection date;
  • source_files.methodology - methodology;
  • source_files.diseaseHpoId - oncological disease ID in HPO database;
  • source_files.oncoStage - oncological disease stage;
  • source_files.oncoSubStage - stage subgroup;
  • source_files.oncoStageDetails - stage details;
  • source_files.therapyLine - therapy line;
  • source_files.pipelineOutdated - whether the pipeline of the sample included in the group analysis was updated after the group analysis creation: true or false;
  • source_files.deleted - whether the sample has been deleted: true or false;
  • source_files.snvsGermlineCalled - whether germline SNVs/Indels discovery was carried out for the sample: true or false;
  • source_files.snvsSomaticCalled - whether somatic SNVs/Indels discovery was carried out for the sample: true or false;
  • source_files.snvsDeleted - whether SNV Viewer data has been deleted: true or false;
  • source_files.cnvsDeleted - whether CNV Viewer data has been deleted: true or false;
  • source_files.needNotifyProcessed - whether the sample processing completion notification was enabled: true or false.

• Fields from Bioinformatic report with information about the sample in which the variant was discovered:

  • source_files.readsCount - the number of reads in the sample file after it was verified, but before cleanup;
  • source_files.finalReadsCount - the number of reads in the sample file counted during the quality check after cleanup;
  • source_files.readsLengthMin - the minimum read length in the sample file;
  • source_files.readsLengthMax - the maximum read length in the sample file;
  • source_files.readsLengthMedian - median length;
  • source_files.cleanupStatus - status of the Check quality and cleanup stage: FINISHED.

• Group analysis information: fields describing the group analysis in which the variant was discovered. These fields generally correspond to those in the "Group Analysis Info" section:

  • group_analysis.name - name;
  • group_analysis.description - comments;
  • group_analysis.type - analysis type: GERMLINE_COHORT, GERMLINE_FAMILY, GERMLINE_POPULATION;
  • group_analysis.archived - whether the group analysis is archived: true or false;
  • group_analysis.outdated - whether group analysis results are outdated: true or false;
  • group_analysis.deleted - whether the group analysis has been deleted: true or false;
  • group_analysis.sequencingType - sequencing type of the sample in group analysis in which the variant was discovered: PANEL, WES, WGS, LOW_PASS_WGS, UNKNOWN.

• Fields with interpreted genetic variant information:

  • snv_user_data.originType - origin: GERMLINE, SOMATIC;
  • snv_user_data.pinned - whether variant is pinned in SNV Viewer: true or false;
  • snv_user_data.pathogenicity - variant pathogenicity: PATHOGENIC, LIKELY_PATHOGENIC, UNCERTAIN_SIGNIFICANCE_CONFLICT, UNCERTAIN_SIGNIFICANCE, LIKELY_BENIGN, BENIGN, UNDEFINED;
  • snv_user_data.pathogenicityOrigin - variant pathogenicity classification origin: ACMG, USER_DEFINED;
  • snv_user_data.pathogenicityApproved - whether variant pathogenicity class is confirmed: true or false;
  • snv_user_data.interpretation - variant interpretation added by the user;
  • snv_user_data.interpretationApproved - whether variant interpretation is confirmed: true or false;
  • snv_user_data.includeToReport - whether variant is included to report: true or false;
  • snv_user_data.mutationClass - mutation class defined by the user for oncorelevant variant in the report;
  • snv_user_data.deleted - whether variant data has been deleted: true or false;
  • snv_user_data.label - variant label: HIGH_SIGNIFICANCE, MODERATE_SIGNIFICANCE, LOW_SIGNIFICANCE, SEQUENCING_ERROR, UNDEFINED;
  • snv_user_data.includeInterpretationResultStatus - potential finding status: INCLUDED_TO_INTERPRETATION_RESULT, EXCLUDED_FROM_POTENTIAL_FINDINGS, UNDEFINED;
  • snv_user_data.interpretationAuthorId - ID of the user who added variant interpretation;
  • partitionId - partition ID in ClickHouse table;
  • Samples info:
    • sources.sample_name - names of the samples, for which the analysis was performed;
    • sources.genotype - genotype;
    • sources.depth - read depth;
    • sources.refReads - reference allele reads count;
    • sources.altReads - alternative allele reads count;
    • sources.allelicFrequency - allelic frequency.

• Variant annotation result fields:

  • genes - the common name of the gene in which the variant is located;
  • originType - mutation type: GERMLINE or SOMATIC;
  • chrId - chromosome number;
  • startDisplay and start - start position;
  • endDisplay and end - end position;
  • refDisplay and ref - reference allele;
  • altDisplay and alt - alternative allele;
  • impact - the predicted effect of the variant on the protein;
  • genomePosition - variant position in the genome;
  • consequences - the effect of the variant on genes;
  • canonicalRefSeqTranscriptId - canonical transcript ID in RefSeq database;
  • rsId - variant ID in dbSNP database;
  • minExon - the number of the first exon affected by the variant;
  • maxExon - the number of the last exon affected by the variant (for a variant affecting one exon, this is the same as the minExon value);
  • vcfFilters - caller filters;
  • hgvsc - nucleotide substitution using the HGVS notation;
  • hgvsp - amino acid substitution using the HGVS notation in the three-letter amino acid code;
  • shortHgvsp - amino acid substitution using the HGVS notation in the single-letter amino acid code;
  • oncoRelevance - whether variant is oncorelevant: true or false;
  • lineOffset - a service field used by the system for internal data processing;
  • cosmicId - variant ID in COSMIC database;
  • ruSeqAf - variant AF in RUSeq database;
  • codingSequenceEffect_aminoAcids - reference amino acid;
  • codingSequenceEffect_cdsPosition - coding sequence position;
  • codingSequenceEffect_codons - nucleotide substitution written as codons;
  • codingSequenceEffect_proteinPosition - protein position;
  • dbnsfpData_aminoAcidPos - amino acid position;
  • dbnsfpData_appris - human splicing isoforms;
  • dbnsfpData_geuvadisEqtlTargetGene - gene from eQTL data analysis in GEUVADIS;
  • phasingGroupData - phasing group information: about the variants included in the phasing group, or about the phasing groups to which the variant belongs;
  • phasingGroupStatus - phasing group status: PHASING_GROUP, PART_OF_GROUP_CONSEQUENCE_EQUAL, PART_OF_GROUP_CONSEQUENCE_UNEQUAL;
  • enigma_clinicalSignificance - variant clinical significance determined by ENIGMA consortium;
  • enigma_clinicalSignificanceComment - comment on clinical significance determined by ENIGMA consortium;
  • customAnnotations - column values from the custom annotations with which the variant was annotated;
  • transcripts - information on gene transcripts in Ensembl database;
  • Protein function effect (polyphenData_score, polyphenData_prediction, dbnsfpData_reliabilityIndex, dbnsfpData_deogenRankscore, dbnsfpDann_score, dbnsfpDann_rankscore, dbnsfpEigen_rawCoding, dbnsfpEigen_rawCodingRankscore, dbnsfpEigen_pcRawCoding, dbnsfpEigen_pcRawCodingRankscore, dbnsfpEigen_pcPhredCoding, dbnsfpFathmm_score, dbnsfpFathmm_convertedRankscore, dbnsfpFathmm_prediction, dbnsfpFathmm_mklCodingScore, dbnsfpFathmm_mklCodingRankscore, dbnsfpFathmm_mklCodingGroupOfFeatures, dbnsfpFathmm_mklCodingPrediction, dbnsfpFathmm_xfCodingScore, dbnsfpFathmm_xfCodingRankscore, dbnsfpFathmm_xfCodingPrediction, dbnsfpLrt_score, dbnsfpLrt_convertedRankscore, dbnsfpLrt_prediction, dbnsfpLrt_omega, dbnsfpMcap_score, dbnsfpMcap_rankscore, dbnsfpMcap_prediction, dbnsfpMeta_svmScore, dbnsfpMeta_svmRankscore, dbnsfpMeta_svmPrediction, dbnsfpMeta_lrScore, dbnsfpMeta_lrRankscore, dbnsfpMeta_lrPrediction, dbnsfpMeta_score, dbnsfpMeta_rankscore, dbnsfpMpc_score, dbnsfpMpc_rankscore, dbnsfpMutPred_score, dbnsfpMutPred_rankscore, dbnsfpMutPred_protId, dbnsfpMutPred_aaChange, dbnsfpMutPred_top5Features, dbnsfpMvp_score, dbnsfpMvp_rankscore, dbnsfpPrimateAi_score, dbnsfpPrimateAi_rankscore, dbnsfpPrimateAi_prediction, dbnsfpBayesDel_addAfPrediction, dbnsfpBayesDel_addAfScore, dbnsfpBayesDel_addAfRankscore, dbnsfpBayesDel_noAfPrediction, dbnsfpBayesDel_noAfScore, dbnsfpBayesDel_noAfRankscore, dbnsfpProvean_score, dbnsfpProvean_convertedRankscore, dbnsfpProvean_prediction, dbnsfpSift_score, dbnsfpSift_convertedRankscore, dbnsfpSift_score4g, dbnsfpSift_convertedRankscore4g, dbnsfpSift_prediction4g, snvCaddData_raw, snvCaddData_phred, snvSpliceAiData_deltaScore, snvSpliceAiData_deltaPosition, snvSpliceAiData_deltaScoreAcceptorGain, snvSpliceAiData_deltaScoreAcceptorLoss, snvSpliceAiData_deltaScoreDonorGain, snvSpliceAiData_deltaScoreDonorLoss, snvSpliceAiData_deltaPositionAcceptorGain, snvSpliceAiData_deltaPositionAcceptorLoss, snvSpliceAiData_deltaPositionDonorGain, snvSpliceAiData_deltaPositionDonorLoss, dbnsfpMutationAssessor_score, dbnsfpMutationAssessor_pred, maxEntScan_alt, maxEntScan_ref, maxEntScan_diff);
  • Allele frequencies in the 1000 Genomes Project (thousandGenomesAfTotal, thousandGenomesData_eastAsianAf, thousandGenomesData_europeanAf, thousandGenomesData_africanAf, thousandGenomesData_americanAf, thousandGenomesData_southAsianAf);
  • Phenotypic significance in ClinVar database (clinvarId, clinvarData_alleleId, clinvarData_clinicalSignificance, clinvarData_clinicalSources, clinvarData_diseaseDatabasesIds, clinvarData_diseaseDatabasesIdsIncl, clinvarData_haplotypeId, clinvarData_origin, clinvarData_phenotypes, clinvarData_phenotypesIncl, clinvarData_reviewStatus);
  • Allele frequencies in gnomAD 3 database (gnomadId, gnomadAfTotal, gnomadData_ac, gnomadData_an, gnomadData_maleAf, gnomadData_femaleAf, gnomadData_ashkenaziJewishAf, gnomadData_ashkenaziJewishMaleAf, gnomadData_ashkenaziJewishFemaleAf, gnomadData_amishAf, gnomadData_amishMaleAf, gnomadData_amishFemaleAf, gnomadData_africanAf, gnomadData_africanMaleAf, gnomadData_africanFemaleAf, gnomadData_finnishAf, gnomadData_finnishMaleAf, gnomadData_finnishFemaleAf, gnomadData_southAsianAf, gnomadData_southAsianMaleAf, gnomadData_southAsianFemaleAf, gnomadData_latinoAf, gnomadData_latinoMaleAf, gnomadData_latinoFemaleAf, gnomadData_nonFinnishEuropeanAfgnomadData_nonFinnishEuropeanMaleAf, gnomadData_nonFinnishEuropeanFemaleAf, gnomadData_eastAsianAf, gnomadData_eastAsianMaleAf, gnomadData_eastAsianFemaleAf, gnomadData_middleEasternAfgnomadData_middleEasternMaleAf, gnomadData_middleEasternFemaleAf, gnomadData_otherAf, gnomadData_otherMaleAf, gnomadData_otherFemaleAf, gnomadData_nhomalt, gnomadData_africanNhomalt, gnomadData_amishNhomalt, gnomadData_latinoNhomalt, gnomadData_ashkenaziJewishNhomalt, gnomadData_eastAsianNhomalt, gnomadData_finnishNhomalt, gnomadData_nonFinnishNhomalt, gnomadData_middleEasternNhomalt, gnomadData_southAsianNhomalt, gnomadData_otherNhomalt, gnomadData_coverage);
  • Allele frequencies in gnomAD 4 database (gnomad4Data_acGenomes, gnomad4Data_acXxGenomes, gnomad4Data_acXyGenomes, gnomad4Data_acJoint, gnomad4Data_acJointXx, gnomad4Data_acJointXy, gnomad4Data_afGenomes, gnomad4Data_afXxGenomes, gnomad4Data_afXyGenomes, gnomad4Data_afJoint, gnomad4Data_afJointXx, gnomad4Data_afJointXy, gnomad4Data_anGenomes, gnomad4Data_anXxGenomes, gnomad4Data_anXyGenomes, gnomad4Data_anJoint, gnomad4Data_anJointXx, gnomad4Data_anJointXy, gnomad4Data_nhomaltGenomes, gnomad4Data_nhomaltXxGenomes, gnomad4Data_nhomaltXyGenomes, gnomad4Data_nhomaltJoint, gnomad4Data_nhomaltJointXx, gnomad4Data_nhomaltJointXy, gnomad4Data_acExomes, gnomad4Data_acXxExomes, gnomad4Data_acXyExomes, gnomad4Data_afExomes, gnomad4Data_afXxExomes, gnomad4Data_afXyExomes, gnomad4Data_anExomes, gnomad4Data_anXxExomes, gnomad4Data_anXyExomes, gnomad4Data_nhomaltExomes, gnomad4Data_nhomaltXxExomes, gnomad4Data_nhomaltXyExomes);
  • Variant conservation (dbnsfpData_ancestralAllele, dbnsfpData_altaiNeandertal, dbnsfpData_denisova, dbnsfpData_vindijiaNeandertal, dbnsfpBstatistic_bValue, dbnsfpBstatistic_rankscore, dbnsfpFitCons_integratedScore, dbnsfpFitCons_integratedRankscore, dbnsfpFitCons_integratedConfidenceValue, dbnsfpFitCons_gm12878Score, dbnsfpFitCons_gm12878Rankscore, dbnsfpFitCons_gm12878ConfidenceValue, dbnsfpFitCons_h1HescScore, dbnsfpFitCons_h1HescRankscore, dbnsfpFitCons_h1HescConfidenceValue, dbnsfpFitCons_huvecScore, dbnsfpFitCons_huvecRankscore, dbnsfpFitCons_huvecConfidenceValue, dbnsfpGerp_neutralRate, dbnsfpGerp_rsScore, dbnsfpGerp_rsRankscore, dbnsfpPhastCons_vertebrate100way, dbnsfpPhastCons_vertebrate100wayRankscore, dbnsfpPhastCons_mammalian30way, dbnsfpPhastCons_mammalian30wayRankscore, dbnsfpPhastCons_primate17way, dbnsfpPhastCons_primate17wayRankscore, dbnsfpPhylop_vertebrate100way, dbnsfpPhylop_vertebrate100wayRankscore, dbnsfpPhylop_mammalian30way, dbnsfpPhylop_mammalian30wayRankscore, dbnsfpPhylop_primate17way, dbnsfpPhylop_primate17wayRankscore, dbnsfpSiphy_pA29way, dbnsfpSiphy_pC29way, dbnsfpSiphy_pG29way, dbnsfpSiphy_pT29way, dbnsfpSiphy_logOdds29way, dbnsfpSiphy_logOdds29wayRankscore);
  • Allele frequencies in ExAC database (dbnsfpExac_ac, dbnsfpExac_af, dbnsfpExac_adjustedAc, dbnsfpExac_adjustedAf, dbnsfpExac_africanAc, dbnsfpExac_africanAf, dbnsfpExac_americanAc, dbnsfpExac_americanAf, dbnsfpExac_eastAsianAc, dbnsfpExac_eastAsianAf, dbnsfpExac_finnishAc, dbnsfpExac_finnishAf, dbnsfpExac_nonFinnishEuropeanAc, dbnsfpExac_nonFinnishEuropeanAf, dbnsfpExac_southAsianAc, dbnsfpExac_southAsianAf, dbnsfpExac_nonTcgaAc, dbnsfpExac_nonTcgaAf, dbnsfpExac_nonTcgaAdjustedAc, dbnsfpExac_nonTcgaAdjustedAf, dbnsfpExac_nonTcgaAfricanAc, dbnsfpExac_nonTcgaAfricanAf, dbnsfpExac_nonTcgaAmericanAc, dbnsfpExac_nonTcgaAmericanAf, dbnsfpExac_nonTcgaEastAsianAc, dbnsfpExac_nonTcgaEastAsianAf, dbnsfpExac_nonTcgaFinnishAc, dbnsfpExac_nonTcgaFinnishAf, dbnsfpExac_nonTcgaNonFinnishEuropeanAc, dbnsfpExac_nonTcgaNonFinnishEuropeanAf, dbnsfpExac_nonTcgaSouthAsianAc, dbnsfpExac_nonTcgaSouthAsianAf, dbnsfpExac_nonPsychAc, dbnsfpExac_nonPsychAf, dbnsfpExac_nonPsychAdjustedAc, dbnsfpExac_nonPsychAdjustedAf, dbnsfpExac_nonPsychAfricanAc, dbnsfpExac_nonPsychAfricanAf, dbnsfpExac_nonPsychAmericanAc, dbnsfpExac_nonPsychAmericanAf, dbnsfpExac_nonPsychEastAsianAc, dbnsfpExac_nonPsychEastAsianAf, dbnsfpExac_nonPsychFinnishAc, dbnsfpExac_nonPsychFinnishAf, dbnsfpExac_nonPsychNonFinnishEuropeanAc, dbnsfpExac_nonPsychNonFinnishEuropeanAf, dbnsfpExac_nonPsychSouthAsianAc, dbnsfpExac_nonPsychSouthAsianAf);
  • Allele frequencies in NHLBI GO ESP (dbnsfpNhlbi_africanAmericanAc, dbnsfpNhlbi_africanAmericanAf, dbnsfpNhlbi_europeanAmericanAc, dbnsfpNhlbi_europeanAmericanAf);
  • Allele frequencies in the UK10K project (dbnsfpUk10_twinsukAc, dbnsfpUk10_twinsukAf, dbnsfpUk10_alspacAc, dbnsfpUk10_alspacAf, dbnsfpUk10_combinedAc, dbnsfpUk10_combinedAf).