Processing error and empty mappings on the LOVD endpoint for `NC_000011.9:g.111742146del`

[ifokkema]

Describe the bug
I ran into some errors while running my data processing pipeline. Apparently, VV can generate mappings to transcripts without actually generating DNA and protein descriptions. The flag value is processing_error, but my library, apparently, didn't pick up on that because no actual messages are included in errors.

To Reproduce
Using the open endpoint so I can link to the output: https://rest.variantvalidator.org/LOVD/lovd/GRCh37/NC_000011.9%3Ag.111742146del/refseq/all/tx/False?content-type=application%2Fjson
Produces (shortened output):

{
  "NC_000011.9:g.111742146del": {
    "NC_000011.9:g.111742146del": {
      "g_hgvs": "NC_000011.9:g.111742146del",
      "genomic_variant_error": null,
      "genomic_variant_warnings": null,
      "hgvs_t_and_p": {
        "NM_001077690.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_001352409.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_001352410.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_001352413.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_001352417.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_001352418.1": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        },
        "NM_024740.2": {
          "p_hgvs_slc": null,
          "p_hgvs_tlc": null,
          "t_hgvs": null,
          "transcript_variant_error": null,
          "transcript_version_warning": null
        }
      }
    },
    "errors": [],
    "flag": "processing_error"
  }
}

Any clue what may be going on? I'm having more variants on other chromosomes where this happens, but I assume it's the same problem. Since all error fields are empty, I really have no clue what might be happening. There are no warnings about alignment gaps, either.

Expected behavior
When an error occurs, having a message will flag my library that there is a problem (although I could update it to do something with the flag, even in the absence of any messages). If the mapping is the issue, removing the mappings would probably be better.

[Peter-J-Freeman]

Hi @ifokkema. This url is no longer maintained. We have deployed a brand new version on https://www181.lamp.le.ac.uk/. We would no longer be able to fix this website and it will go down very soon and be diverted to the new server. We really need to have the links and testing done there are we have made substantial improvements.

[Peter-J-Freeman]

@ifokkema, I found the bug for this variant and it will be fixed in the next release to

OrderedDict({'NC_000011.9:g.111742146delG': OrderedDict({'errors': [], 'flag': None, 'NC_000011.9:g.111742146delG': OrderedDict({'p_vcf': '11:111742145:CG:C', 'g_hgvs': 'NC_000011.9:g.111742146del', 'selected_build': 'GRCh37', 'genomic_variant_error': None, 'genomic_variant_warnings': None, 'hgvs_t_and_p': {'NM_001352418.1': OrderedDict({'t_hgvs': 'NM_001352418.1:c.59_61=', 'p_hgvs_tlc': None, 'p_hgvs_slc': None, 'select_status': {}, 'gene_info': {'symbol': 'ALG9', 'hgnc_id': 'HGNC:15672'}, 'transcript_version_warning': None, 'gapped_alignment_warning': 'GappedAlignmentWarning: Submitted description does not represent a true variant because it is an artefact of aligning NM_001352418.1 with NC_000011.9 (genome build GRCh37)', 'gap_statement': 'GappedAlignmentWarning: NM_001352418.1 contains 1 fewer bases between c.60_61 than NC_000011.9', 'transcript_variant_error': None, 'primary_assembly_loci': {'grch37': {'NC_000011.9': {'hgvs_genomic_description': 'NC_000011.9:g.111742146del', 'vcf': {'chr': '11', 'pos': '111742145', 'ref': 'CG', 'alt': 'C'}}}, 'hg19': {'NC_000011.9': {'hgvs_genomic_description': 'NC_000011.9:g.111742146del', 'vcf': {'chr': 'chr11', 'pos': '111742145', 'ref': 'CG', 'alt': 'C'}}}}, 'alt_genomic_loci': []})}})}), 'metadata': {'variantvalidator_version': '4.0.1.dev100+g0f5e4f065.d20260730', 'variantvalidator_hgvs_version': '4.0.0', 'vvta_version': 'vvta_2026_07', 'vvseqrepo_db': 'VV_SR_2026_07/master', 'vvdb_version': 'vvdb_2026_7', 'variantformatter_version': '4.0.1.dev97+gf93df2717.d20260728'}})

Any others?