NG_053115.1:g.4659_4750delinsT causes server error

[leicray]

Describe the bug
A user has been repeatedly trying to validate the variant NG_053115.1:g.4659_4750delinsT. The variant does not validate for GRCh37 or GRCh38 and results in ERROR messages being sent to the sysadmins.

The on-screen error messages are:

Unable to validate the submitted variant NG_053115.1:g.4659_4750delinsT against the GRCh37 assembly.

and

Unable to validate the submitted variant NG_053115.1:g.4659_4750delinsT against the GRCh38 assembly.

Reference sequence NG_053115.1 is valid and corresponds to the ODAD4 gene. The corresponding MANE Select transcript is NM_031421.5.

Although it's not entirely reproducible, failed attempts to validate this variant description seem to interfere with subsequent attempts to validate variant descriptions that are known to be valid.

[Peter-J-Freeman]

seems this has no aligned transcripts in our database nor is the RefSeqGene record in the database.

{
"flag": "intergenic",
"intergenic_variant_1": {
"alt_genomic_loci": [],
"annotations": {},
"gene_ids": {},
"gene_symbol": "none",
"genome_context_intronic_sequence": "",
"hgvs_lrg_transcript_variant": "",
"hgvs_lrg_variant": "",
"hgvs_predicted_protein_consequence": {
"lrg_slr": "",
"lrg_tlr": "",
"slr": "",
"tlr": ""
},
"hgvs_refseqgene_variant": "NG_053115.1:g.4659_4749del",
"hgvs_transcript_variant": "",
"primary_assembly_loci": {},
"reference_sequence_records": {
"refseqgene": "https://www.ncbi.nlm.nih.gov/nuccore/NG_053115.1"
},
"refseqgene_context_intronic_sequence": "",
"rna_variant_descriptions": null,
"selected_assembly": "GRCh37",
"submitted_variant": "NG_053115.1:g.4659_4750delinsT",
"transcript_description": "",
"validation_warnings": [
"No transcripts found that fully overlap the described variation in the genomic sequence",
"Mapping unavailable for RefSeqGene NG_053115.1:g.4659_4750delinsT using alignment method = splign"
],
"variant_exonic_positions": null
},
"metadata": {
"variantvalidator_hgvs_version": "2.2.0",
"variantvalidator_version": "2.2.1.dev709+g6340024",
"vvdb_version": "vvdb_2024_12",
"vvseqrepo_db": "VV_SR_2024_09/master",
"vvta_version": "vvta_2024_09"
}
}