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.

2KB

variants_batch_template_GRCh37.csv

Open

2KB

variants_batch_template_GRCh38.csv

Open

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.

Field (column name)	SNV	CNV
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:

• Pathogenicity

• Disease

• Interpretation

• Notes

• Transcript

• ACMG applied

• ACMG not met

• Update

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

Field (column) name

Field details

Expected input

Example

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

Field (column) name	Field details	Expected input	Example
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