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‎docs/variant-queries.md‎

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Range queries require the use of **single** `start` and `end` parameters, in contrast
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to _Bracket Queries_.
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#### Example: Any variant affecting _EIF4A1_
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#### Example: Any variant affecting _EIF4A1_
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=== "Beacon v2 GET"
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This table is maintained in parallel with the [hCNV community documentation](https://cnvar.org/resources/CNV-annotation-standards/#cnv-term-use-comparison-in-computational-fileschema-formats).
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| [EFO](http://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS](https://vrs.ga4gh.org/en/latest/terms_and_model.html#copynumberchange)[^1] | Notes |
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| ------------------------------------------- | ------------------------------------------------------------------------------ | -------------------------------------------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | ----- |
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| <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030070`](http://www.ebi.ac.uk/efo/EFO_0030070) gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
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| [`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030071`](http://www.ebi.ac.uk/efo/EFO_0030071)</nobr> low-level gain | |
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| [`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
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| [`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](http://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](http://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | <nobr>[`EFO:0030072`](http://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain[^4] | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
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| [`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030067`](http://www.ebi.ac.uk/efo/EFO_0030067)</nobr> loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
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| [`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030068`](http://www.ebi.ac.uk/efo/EFO_0030068)</nobr> low-level loss | |
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| [`EFO:0020073`](http://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
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| [`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](http://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | <nobr>[`EFO:0030069`](http://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |
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##### Last updated 2023-07-13 to align with 2023-03-22 hCNV documentation (VRS 1.3 adjustment) by @mbaudis
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| [EFO](https://www.ebi.ac.uk/efo/EFO_0030063) | Beacon | [VCF](https://samtools.github.io/hts-specs/) | SO | GA4GH [VRS 2.n](https://vrs.ga4gh.org/en/latest/concepts/SystemicVariation/CopyNumberChange.html)| GA4GH VRS 1.3[^1] | Notes |
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| --------- | ------ | ---------- | ---| -------------------- | ----------------- | ----- |
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| <nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | gain | <nobr>[`EFO:0030070`](https://www.ebi.ac.uk/efo/EFO_0030070) gain | a sequence alteration whereby the copy number of a given genomic region is greater than the reference sequence |
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| [`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071) low-level copy number gain| `DUP`[^2] or<br/><nobr>[`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | low-level gain | <nobr>[`EFO:0030071`](https://www.ebi.ac.uk/efo/EFO_0030071)</nobr> low-level gain | |
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| [`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072) high-level copy number gain | `DUP`[^2] or<br/><nobr>[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | high-level gain | <nobr>[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain | commonly but not consistently used for >=5 copies on a bi-allelic genome region |
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| [`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073) focal genome amplification | `DUP`[^2] or<br/><nobr>[`EFO:0030073`](https://www.ebi.ac.uk/efo/EFO_0030073)</nobr> | `DUP`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001742`](https://www.sequenceontology.org/browser/current_release/term/SO:0001742) copy_number_gain | high-level gain | <nobr>[`EFO:0030072`](https://www.ebi.ac.uk/efo/EFO_0030072)</nobr> high-level gain[^4] | commonly but not consistently used for >=5 copies on a bi-allelic genome region, of limited size (operationally max. 1-5Mb) |
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| [`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067) copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | loss | <nobr>[`EFO:0030067`](https://www.ebi.ac.uk/efo/EFO_0030067)</nobr> loss | a sequence alteration whereby the copy number of a given genomic region is smaller than the reference sequence |
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| [`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068) low-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | low-level loss | <nobr>[`EFO:0030068`](https://www.ebi.ac.uk/efo/EFO_0030068)</nobr> low-level loss | |
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| [`EFO:0020073`](https://www.ebi.ac.uk/efo/EFO_0020073) high-level copy number loss | `DEL`[^2] or<br/><nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | high-level loss | <nobr>[`EFO:0020073`](https://github.com/EBISPOT/efo/issues/1941)</nobr> high-level loss | a loss of several copies; also used in cases where a complete genomic deletion cannot be asserted |
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| [`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069) complete genomic deletion | `DEL`[^2] or<br/><nobr>[`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069)</nobr> | `DEL`<br/><nobr>`SVCLAIM=D`[^3]</nobr> | [`SO:0001743`](https://www.sequenceontology.org/browser/current_release/term/SO:0001743) copy_number_loss | complete genomic loss | <nobr>[`EFO:0030069`](https://www.ebi.ac.uk/efo/EFO_0030069)</nobr> complete genomic loss | complete genomic deletion (e.g. homozygous deletion on a bi-allelic genome region) |
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##### Last updated 2025-08-08 by @mbaudis (VRS 2 adjustment)
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##### updated 2023-03-20 by @mbaudis (VRS proposal)
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## Query Parameter Change Log

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