CSV format requirements for variant upload
Use a CSV file to batch upload variants into Curate. Batch upload has long supported adding new variants; starting with v100.40.0, batch upload also supports updating existing variants using the Update field.
Batch upload supports SNV, indel, mtDNA, and CNV variants. Each row in the CSV represents a single variant and is validated during upload to ensure required fields, formats, and permissions are met before the variant is added or updated.
Starting with v100.40.0, batch upload also supports importing ACMG evidence for SNV, indel, and mtDNA variants using the ACMG applied and ACMG not met fields.
General CSV format requirements
A CSV file used to add or update variants in Curate must meet the following requirements:
File extension: .csv.
The first row contains column headers.
Each column represents a data field.
Column headers are case-sensitive and exactly match this specification or a template.
Each row after the header represents a variant.
There are no empty rows between the header row and variant rows and between variant rows.
Maximum file size: 10 MB.
Maximum number of variants: 5000.
Supported variant types:
SNV (SNV, indel)
mtDNA
CNV (DEL, DUP)
SNV and CNV rows may be included in the same file if all mandatory fields are present (see Field summary).
CSV file templates
You can use the templates below as a starting point.
Field summary
The table below summarizes which fields are supported for each variant type and whether they are mandatory or optional.
Mandatory fields are required to add or update a variant.
Optional fields may be included if applicable.
Vartype
Mandatory
Mandatory
Chromosome
Mandatory
Mandatory
Position
Mandatory
Mandatory
REF
Mandatory
Mandatory
ALT
Mandatory
N/A
End
N/A
Mandatory
Overlap
N/A
Optional
Pathogenicity
Optional
Optional
Disease
Optional
Optional
Interpretation
Optional
Optional
Notes
Optional
Optional
Transcript
Optional
N/A
ACMG applied (v100.40.0+)
Optional
N/A
ACMG not met (v100.40.0+)
Optional
N/A
Update (v100.40.0+)
Optional
Optional
Access-controlled fields
Some optional fields require specific user permissions to update.
Access-controlled fields include:
PathogenicityDiseaseInterpretationNotesTranscriptACMG appliedACMG not metUpdate
If you do not have permission to update a field:
Curate ignores the field.
The variant is still added or updated where possible.
The upload summary in the last step of multiple variant upload marks the variant as Partial Success and lists the ignored fields.
Batch variant CSV file validation rules
Curate validates each CSV file before upload, and the validation rules vary by variant type. The tables below list the supported fields for each variant type, including mandatory fields (in red font) and optional fields for both new variants and updates.
Single nucleotide variants
The fields for an SNV, indel, or mtDNA variant should be filled in according to the rules in the table.
Table 1. Validation rules for SNV fields
Vartype
Mandatory.
SNV.
Applicable for both SNV and indel.
SNV
Chromosome
Mandatory.
1 - 22, X, Y, M
3
Position
Mandatory.
Integer
123000
REF
Mandatory.
A, T, G, C, or a string of these letters
G
ALT
Mandatory.
A, T, G, C, or a string of these letters
GACT
Pathogenicity
Optional. Access-controlled.
Pathogenic, Likely pathogenic, VUS, Likely benign, Benign
Likely pathogenic
Disease
Optional. OMIM ID.
Integer
113705
Interpretation
Optional. Access-controlled.
Free text under 65000 characters
Free text
Notes
Optional. Access-controlled.
Free text under 65000 characters
Free text
Transcript
Optional. Access-controlled. NCBI RefSeq transcript ID.
NCBI RefSeq transcript ID
NM_000183.3
ACMG applied (v100.40.0+)
Optional.
Access-controlled.
ACMG tags applied to the variant.
If a tag is not listed under ACMG applied or ACMG not met, it remains inactive for the variant.
Comma-separated list of <tag> or <tag>_<strength> entries.
Recognized <strength> values: Supporting, Moderate, Strong, Very_Strong, Stand_Alone.
If a <tag> is provided without an explicit <strength>, the system applies the default ACMG strength.
PVS1, PM2_Supporting
ACMG not met (v100.40.0+)
Optional.
Access-controlled.
ACMG tags explicitly excluded for the variant.
If a tag is not listed under ACMG applied or ACMG not met, it remains inactive for the variant.
Comma-separated list of <tag> entries.
BS1, BP4
Update
(v100.40.0+)
Optional.
Access-controlled.
When set to true, triggers variant information update.
Default value is false.
true, false
true
Copy number variants
Fill the fields for a CNV variant according to the rules defined in the validation table.
Table 2. Validation rules for CNV fields
Vartype
Mandatory.
DEL, DUP
DEL
Chromosome
Mandatory.
Integer
3
Position
Mandatory.
Integer
123000
End
Mandatory.
Integer greater than Position
124000
REF
Mandatory.
A, T, G, C
G
Overlap
Optional: if absent or empty, the fallback value 70 is assigned.
Integer 0-100
80
Pathogenicity
Optional. Access-controlled.
Pathogenic, Likely pathogenic, VUS, Likely benign, Benign
Likely pathogenic
Disease
Optional. Access-controlled. OMIM ID.
Integer
113705
Interpretation
Optional. Access-controlled.
Free text under 65000 characters
Free text
Notes
Optional. Access-controlled.
Free text under 65000 characters
Free text
Update
(v100.40.0+)
Optional. Access-controlled.
When set to true, triggers variant information update.
Default value is false.
true, false
true
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