The registry should ask the individual to upload (if the registry’s platform supports this) or send a copy of their genetic report to confirm their diagnosis and enter the data collected in the following items. Furthermore, the name and location of the genetic testing centre should be collected locally, as this will allow curators to request a copy of the genetic report if it is not immediately available or to request further clarification or information if needed (permission to do this should be sought within the consent process where applicable).
Specifies whether the diagnosis has been genetically confirmed. If the genetic test results are pending, the value must be No.
This item refers to a diagnosis of 5q SMA. If the value is Yes, the results must be captured in one or more instances of the record Genetic report.
| Item type: | yes/no |
| Consistency rules: | Must be |
| Related items in previous version: | 4.00 |
| Usage in other datasets: | DMDLGMD |
In version 2.0, it was clarified that this item applies to 5q SMA.
Specifies whether the diagnosis was made as a result of screening.
This item refers to a diagnosis of 5q SMA.
| Item type: | single selection |
| Related items in previous version: | 4.01 |
| Usage in other datasets: | DMD |
In version 2.1, it was clarified that this item refers to a diagnosis of 5q SMA.
The datestamp of this record must be the date of the genetic report. All information collected in this record should be extracted from the genetic report and confirmed with a geneticist if necessary.
| Related items in previous version: | 4.04 |
Since version 2.1, this record is no longer longitudinal and the item Genetic report date was added instead.
| Item type: | single selection |
| Related items in previous version: | 4.05 |
In version 2.0, the following changes were applied:
Homozygous substitution was added.Description of the variant according to HGVS nomenclature.
The variant described here must be located in the SMN1 gene. The value must be collected only if the variant includes a substitution (point mutation), i.e. SMN1 variant is either Compound heterozygous deletion exon 7, Compound heterozygous substitutions or Homozygous substitution. Otherwise it should be collected. If the reference sequence is known, it must be included.
Examples:
NM_000344.3:c.[824_834del];[815A>G] for a compound heterozygous deletion of exon 7 and a substitutionNM_000344.3:c.[c.815A>C];[c.821C>T] for compound heterozygous substitutions| Item type: | restricted text |
| Usage in other datasets: | DMDLGMD |
This item was added in version 2.0 to allow providing details in case of a substitution.
Testing method used to obtain the genetic result.
Registries may add an additional free-text field in their data collections forms to capture possible methods other than the ones provided in this item; values in the free-text field should be checked by a curator and mapped to the provided values wherever possible. New methods may be added to the dataset by TREAT-NMD whenever appropriate.
This item refers to the testing method used to obtain the result provided in SMN1 variant and SMN1 variant HGVS.
| Item type: | single selection |
| Related items in previous version: | 4.06 |
| Usage in other datasets: | DMD |
In version 2.0, the option for other methods and the associated implicit free-text field were removed. However, registries may include them in their data collection forms as noted above.
SMN2 copy number following the following format:
| Item type: | restricted text |
| Related items in previous version: | 4.09 |
In version 2.0, the type was changed to restricted text with the specified format in order to allow providing ranges when the precise number is unknown.
Testing method used to obtain the genetic result.
Registries may add an additional free-text field in their data collections forms to capture possible methods other than the ones provided in this item; values in the free-text field should be checked by a curator and mapped to the provided values wherever possible. New methods may be added to the dataset by TREAT-NMD whenever appropriate.
This item refers to the testing method used to obtain the result provided in SMN2 copy number.
| Item type: | single selection |
| Related items in previous version: | 4.08 |
| Usage in other datasets: | DMD |
In version 2.0, the option for other methods and the associated implicit free-text field were removed. However, registries may include them in their data collection forms as noted above.
Specifies whether the variant c.859G>C is present in the SMN2 gene. Yes means that the variant was found, No means that the variant was checked for but not found.
The ID of this item does not contain the period and the character '>' because they are not valid characters for identifiers in many software environments. Data collection forms should display the HGVS-compliant variant description “c.859G>C” in questions or labels.
| Item type: | yes/no |
This item was added in version 2.0.
Testing method used to obtain the genetic result.
Registries may add an additional free-text field in their data collections forms to capture possible methods other than the ones provided in this item; values in the free-text field should be checked by a curator and mapped to the provided values wherever possible. New methods may be added to the dataset by TREAT-NMD whenever appropriate.
This item refers to the testing method used to obtain the result provided in SMN2 variant c859GtoC.
| Item type: | single selection |
| Usage in other datasets: | DMD |
This item was added in version 2.0.