SACGF / SACGF/variantgrid

Clingen HGVS requests for variants that are too long

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#1,222 14 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
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Description

Uploading structural variants (in 38), the logs are full of:

```
Could not convert '1:12824541 A>ATAACT ....

using HGVSConverterType.CLINGEN_ALLELE_REGISTRY: Error contacting ClinGen Allele Registry. Method: 'GET', Response: 400, JSON: description: Variation given on the input is too long. There is 10000 bp limit for variation's length., errorType: VariationTooLong, hgvs: , length: 33538, message: VariationTooLong
[2025-01-08 11:40:08,220: WARNING/ForkPoolWorker-4] response_json={'description': "Variation given on the input is too long. There is 10000 bp limit for variation's length.", 'errorType': 'VariationTooLong', 'hgvs': '', 'length': '33538', 'message': 'VariationTooLong'}
```

We should be able to tell that these are too long and not send them

We have this on variants - ```can_have_clingen_allele``` but probably not on VariantCoordinate - called via:

```
annotation.vcf_files.bulk_vep_vcf_annotation_inserter.BulkVEPVCFAnnotationInserter._add_hgvs_c
hgvs_matcher.variant_coordinate_to_hgvs_variant
```

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