Sometimes rest VV returns results unrelated to query

[vidboda]

Sometimes, but quite often indeed, VV returns results that are totally unrelated from the initial query.

For example, today I submitted this query using the swagger UI at https://rest.variantvalidator.org/:

https://rest.variantvalidator.org/VariantValidator/variantvalidator/**hg19**/**15**-43921089-C-T/all?content-type=application%2Fjson

and got as results a variant located on chr12:

"selected_assembly": "GRCh38",
"submitted_variant": "NM_015409.5:c.4421C>T",
"transcript_description": "Homo sapiens E1A binding protein p400 (EP400), mRNA",
"validation_warnings": [
"RefSeqGene record not available"
],
"variant_exonic_positions": {
"NC_000012.11": {
"end_exon": "22",
"start_exon": "22"
},
"NC_000012.12": {
"end_exon": "22",
"start_exon": "22"
}
}

Other examples seen today returned by MobiDetails (still using the REST API):

• VV check failed for variant NM_015454.3:c.-2-243G>A with args: {'NM_003104.5:c.927G>A': {...} which means the user tried to validate a variant lying on gene LARP7 on chr4 and got results for a variant lying in gene SORD on chr15. (15h23)
• VV check failed for variant NM_002735.3:c.253A>C with args: {'NM_001330609.1:c.203C>T': {...} : variant asked on PRKAR1B on chr7 and results for WASHC5 on chr8 (15h06)

The error seems to occur whatever the select assembly is (hg19, hg38, GRCh37, GRCh38).

[Peter-J-Freeman]

I have had a think about how we might handle this programatically

Did you by any chance keep a full json for one of these errors???? @beboche. If so, please can you place it below. Please also include the API call.

[vidboda]

I have two of these from yesterday:

https://rest.variantvalidator.org/VariantValidator/variantvalidator/GRCh38/NM_002735.3:c.253A>C/all?content-type=application/json

{'NM_001330609.1:c.203C>T': {'alt_genomic_loci': [], 'annotations': {'chromosome': '8', 'db_xref': {'CCDS': 'CCDS83325.1', 'ensemblgene': None, 'hgnc': 'HGNC:28984', 'ncbigene': '9897', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '8q24.13', 'note': 'WASH complex subunit 5', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS83325', 'CCDS6355'], 'ensembl_gene_id': 'ENSG00000164961', 'entrez_gene_id': '9897', 'hgnc_id': 'HGNC:28984', 'omim_id': ['610657'], 'ucsc_id': 'uc003yrt.4'}, 'gene_symbol': 'WASHC5', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_001317538.1:p.(P68L)', 'tlr': 'NP_001317538.1:p.(Pro68Leu)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_001330609.1:c.203C>T', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000008.10:g.126091044G>A', 'vcf': {'alt': 'A', 'chr': '8', 'pos': '126091044', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000008.11:g.125078802G>A', 'vcf': {'alt': 'A', 'chr': '8', 'pos': '125078802', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000008.10:g.126091044G>A', 'vcf': {'alt': 'A', 'chr': 'chr8', 'pos': '126091044', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000008.11:g.125078802G>A', 'vcf': {'alt': 'A', 'chr': 'chr8', 'pos': '125078802', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': '[https://www.ncbi.nlm.nih.gov/nuccore/NP_001317538.1](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NP_001317538.1__;!!DV4KuIgKKrh48VMFxQ!Vdw0Sv5QSeylWP_y_n1o3XZV7VGFPYF099b_v6kVbkM0VR8rKUod9TDSkbHhBHZV_wvuF-vR$)', 'transcript': '[https://www.ncbi.nlm.nih.gov/nuccore/NM_001330609.1](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NM_001330609.1__;!!DV4KuIgKKrh48VMFxQ!Vdw0Sv5QSeylWP_y_n1o3XZV7VGFPYF099b_v6kVbkM0VR8rKUod9TDSkbHhBHZV_8npKy6i$)'}, 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000008.11:g.125078802G>A', 'transcript_description': 'Homo sapiens WASH complex subunit 5 (WASHC5), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001330609.1 is available (NM_001330609.2): NM_001330609.2:c.203C>T MUST be fully validated prior to use in reports: select_variants=NM_001330609.2:c.203C>T', 'RefSeqGene record not available'], 'variant_exonic_positions': {'NC_000008.10': {'end_exon': '5', 'start_exon': '5'}, 'NC_000008.11': {'end_exon': '5', 'start_exon': '5'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.0.1', 'variantvalidator_version': '2.0.1.dev31+g31426d1', 'vvdb_version': 'vvdb_2021_4', 'vvseqrepo_db': 'VV_SR_2021_2/master', 'vvta_version': 'vvta_2021_2'}, 'validation_warning_1': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000008.11:g.125078802G>A', 'transcript_description': '', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001330609.1 is available (NM_001330609.2): NM_001330609.2:c.203C>T MUST be fully validated prior to use in reports: select_variants=NM_001330609.2:c.203C>T', 'RefSeqGene record not available'], 'variant_exonic_positions': None}, 'validation_warning_2': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000008.11:g.125078802G>A', 'transcript_description': '', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001330609.1 is available (NM_001330609.2): NM_001330609.2:c.203C>T MUST be fully validated prior to use in reports: select_variants=NM_001330609.2:c.203C>T', 'RefSeqGene record not available'], 'variant_exonic_positions': None}, 'validation_warning_3': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000008.11:g.125078802G>A', 'transcript_description': '', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001330609.1 is available (NM_001330609.2): NM_001330609.2:c.203C>T MUST be fully validated prior to use in reports: select_variants=NM_001330609.2:c.203C>T', 'RefSeqGene record not available'], 'variant_exonic_positions': None}}

and

https://rest.variantvalidator.org/VariantValidator/variantvalidator/GRCh38/NM_015454.3:c.-2-243G>A/all?content-type=application/json

{'NM_003104.5:c.927G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '15', 'db_xref': {'CCDS': 'CCDS10116.1', 'ensemblgene': None, 'hgnc': 'HGNC:11184', 'ncbigene': '6652', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '15q21.1', 'note': 'sorbitol dehydrogenase', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS10116'], 'ensembl_gene_id': 'ENSG00000140263', 'entrez_gene_id': '6652', 'hgnc_id': 'HGNC:11184', 'omim_id': ['182500'], 'ucsc_id': 'uc001zul.5'}, 'gene_symbol': 'SORD', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_003095.2:p.(S309=)', 'tlr': 'NP_003095.2:p.(Ser309=)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_003104.5:c.927G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000015.9:g.45365581G>A', 'vcf': {'alt': 'A', 'chr': '15', 'pos': '45365581', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000015.10:g.45073383G>A', 'vcf': {'alt': 'A', 'chr': '15', 'pos': '45073383', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000015.9:g.45365581G>A', 'vcf': {'alt': 'A', 'chr': 'chr15', 'pos': '45365581', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000015.10:g.45073383G>A', 'vcf': {'alt': 'A', 'chr': 'chr15', 'pos': '45073383', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': '[https://www.ncbi.nlm.nih.gov/nuccore/NP_003095.2](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NP_003095.2__;!!DV4KuIgKKrh48VMFxQ!T6l70sxNuHgtWpxc6xsEnkXC3JVE73qa3QSQeyaKufpvFJOs6kde5KPJaKjYiMrZOKC6pH_D$)', 'transcript': '[https://www.ncbi.nlm.nih.gov/nuccore/NM_003104.5](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NM_003104.5__;!!DV4KuIgKKrh48VMFxQ!T6l70sxNuHgtWpxc6xsEnkXC3JVE73qa3QSQeyaKufpvFJOs6kde5KPJaKjYiMrZOOY6J1Sb$)'}, 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000015.10:g.45073383G>A', 'transcript_description': 'Homo sapiens sorbitol dehydrogenase (SORD), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_003104.5 is available (NM_003104.6): NM_003104.6:c.927G>A MUST be fully validated prior to use in reports: select_variants=NM_003104.6:c.927G>A', 'RefSeqGene record not available'], 'variant_exonic_positions': {'NC_000015.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000015.9': {'end_exon': '9', 'start_exon': '9'}}}, 'NM_003104.6:c.927G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '15', 'db_xref': {'CCDS': 'CCDS10116.1', 'ensemblgene': None, 'hgnc': 'HGNC:11184', 'ncbigene': '6652', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '15q21.1', 'note': 'sorbitol dehydrogenase', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS10116'], 'ensembl_gene_id': 'ENSG00000140263', 'entrez_gene_id': '6652', 'hgnc_id': 'HGNC:11184', 'omim_id': ['182500'], 'ucsc_id': 'uc001zul.5'}, 'gene_symbol': 'SORD', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_003095.2:p.(S309=)', 'tlr': 'NP_003095.2:p.(Ser309=)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_003104.6:c.927G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000015.9:g.45365581G>A', 'vcf': {'alt': 'A', 'chr': '15', 'pos': '45365581', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000015.10:g.45073383G>A', 'vcf': {'alt': 'A', 'chr': '15', 'pos': '45073383', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000015.9:g.45365581G>A', 'vcf': {'alt': 'A', 'chr': 'chr15', 'pos': '45365581', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000015.10:g.45073383G>A', 'vcf': {'alt': 'A', 'chr': 'chr15', 'pos': '45073383', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': '[https://www.ncbi.nlm.nih.gov/nuccore/NP_003095.2](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NP_003095.2__;!!DV4KuIgKKrh48VMFxQ!T6l70sxNuHgtWpxc6xsEnkXC3JVE73qa3QSQeyaKufpvFJOs6kde5KPJaKjYiMrZOKC6pH_D$)', 'transcript': '[https://www.ncbi.nlm.nih.gov/nuccore/NM_003104.6](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NM_003104.6__;!!DV4KuIgKKrh48VMFxQ!T6l70sxNuHgtWpxc6xsEnkXC3JVE73qa3QSQeyaKufpvFJOs6kde5KPJaKjYiMrZOCaCpoHT$)'}, 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000015.10:g.45073383G>A', 'transcript_description': 'Homo sapiens sorbitol dehydrogenase (SORD), transcript variant 1, mRNA', 'validation_warnings': ['RefSeqGene record not available'], 'variant_exonic_positions': {'NC_000015.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000015.9': {'end_exon': '9', 'start_exon': '9'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.0.1', 'variantvalidator_version': '2.0.1.dev31+g31426d1', 'vvdb_version': 'vvdb_2021_4', 'vvseqrepo_db': 'VV_SR_2021_2/master', 'vvta_version': 'vvta_2021_2'}, 'validation_warning_1': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000015.10:g.45073383G>A', 'transcript_description': '', 'validation_warnings': ['A more recent version of the selected reference sequence NM_003104.5 is available (NM_003104.6): NM_003104.6:c.927G>A MUST be fully validated prior to use in reports: select_variants=NM_003104.6:c.927G>A', 'RefSeqGene record not available'], 'variant_exonic_positions': None}, 'validation_warning_2': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NC_000015.10:g.45073383G>A', 'transcript_description': '', 'validation_warnings': ['A more recent version of the selected reference sequence NM_003104.5 is available (NM_003104.6): NM_003104.6:c.927G>A MUST be fully validated prior to use in reports: select_variants=NM_003104.6:c.927G>A', 'RefSeqGene record not available'], 'variant_exonic_positions': None}}

[Peter-J-Freeman]

Thanks. I will see if I can think of a work around

So, in case 1, the input is NM_002735.3:c.253A>C but the output comes in the context of NM_001330609.1:c.203C>T and thinks the submitted variant is 'submitted_variant': 'NC_000008.11:g.125078802G>A'

So, if I capture the input variant description and it does not match the displayed submitted variant, re-validate before returning. Sounds like it's worth a try

[ifokkema]

Pete, is this a race condition somewhere? Are you communicating over one port with multiple processes or so?

[Peter-J-Freeman]

No idea @ifokkema . I have to say that the server stuff is not something I've had much chance to get to know. Thanks for the hint, this is possible. I do have multi processes and multi threading running. Think there might be 1 port. Can I send you the configs??

[vidboda]

Hi,

a new one just occured:

https://rest.variantvalidator.org/VariantValidator/variantvalidator/GRCh38/NM_001304808.3:c.2066C>T/all?content-type=application/json

{'NM_000548.5:c.4422_4423del': {'alt_genomic_loci': [], 'annotations': {'chromosome': '16', 'db_xref': {'CCDS': 'CCDS10458.1', 'ensemblgene': None, 'hgnc': 'HGNC:12363', 'ncbigene': '7249', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '16p13.3', 'note': 'TSC complex subunit 2', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS10458', 'CCDS45384', 'CCDS81934', 'CCDS81933', 'CCDS81932', 'CCDS58408', 'CCDS10459'], 'ensembl_gene_id': 'ENSG00000103197', 'entrez_gene_id': '7249', 'hgnc_id': 'HGNC:12363', 'omim_id': ['191092'], 'ucsc_id': 'uc002con.4'}, 'gene_symbol': 'TSC2', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_487p1:p.(R1474Sfs*49)', 'lrg_tlr': 'LRG_487p1:p.(Arg1474SerfsTer49)', 'slr': 'NP_000539.2:p.(R1474Sfs*49)', 'tlr': 'NP_000539.2:p.(Arg1474SerfsTer49)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_000548.5:c.4422_4423del', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000016.9:g.2134645_2134646del', 'vcf': {'alt': 'A', 'chr': '16', 'pos': '2134640', 'ref': 'AAG'}}, 'grch38': {'hgvs_genomic_description': 'NC_000016.10:g.2084644_2084645del', 'vcf': {'alt': 'A', 'chr': '16', 'pos': '2084639', 'ref': 'AAG'}}, 'hg19': {'hgvs_genomic_description': 'NC_000016.9:g.2134645_2134646del', 'vcf': {'alt': 'A', 'chr': 'chr16', 'pos': '2134640', 'ref': 'AAG'}}, 'hg38': {'hgvs_genomic_description': 'NC_000016.10:g.2084644_2084645del', 'vcf': {'alt': 'A', 'chr': 'chr16', 'pos': '2084639', 'ref': 'AAG'}}}, 'reference_sequence_records': {'protein': '[https://www.ncbi.nlm.nih.gov/nuccore/NP_000539.2](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NP_000539.2__;!!DV4KuIgKKrh48VMFxQ!STwBu38DR6QqG28dkkRR37qPe48SBChqrTHCdK_M5I8iISAfqmP1zMAN-tY434XJf4wIctM_$)', 'transcript': '[https://www.ncbi.nlm.nih.gov/nuccore/NM_000548.5](https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/nuccore/NM_000548.5__;!!DV4KuIgKKrh48VMFxQ!STwBu38DR6QqG28dkkRR37qPe48SBChqrTHCdK_M5I8iISAfqmP1zMAN-tY434XJf5oD8cYk$)'}, 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NM_000548.5:c.4422_4423del', 'transcript_description': 'Homo sapiens TSC complex subunit 2 (TSC2), transcript variant 1, mRNA', 'validation_warnings': ['RefSeqGene record not available'], 'variant_exonic_positions': {'NC_000016.10': {'end_exon': '34', 'start_exon': '34'}, 'NC_000016.9': {'end_exon': '34', 'start_exon': '34'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.0.1', 'variantvalidator_version': '2.0.1.dev41+g9de1da3', 'vvdb_version': 'vvdb_2021_4', 'vvseqrepo_db': 'VV_SR_2021_2/master', 'vvta_version': 'vvta_2021_2'}}

[ifokkema]

Thanks for the hint, this is possible. I do have multi processes and multi threading running. Think there might be 1 port. Can I send you the configs??

I think I'd need more than just the configs to understand the whole structure of the system. I know next to nothing about the internal works of VV, and I can't say if this is "server stuff" or "VV stuff". The thing to look for is shared connections or ports; so, e.g., how the API connects to the main VV process that does the analysis. If files are created and then read, that's always a weak spot. Or multiple processes talking to one program that doesn't have a way to know what process it's replying to. Since even the submitted_variant key is wrong, whatever part of the code that keeps this variable in memory while other stuff is calculated is already behind some connection that gets mixed up. So the problem is between the high-level API request handling and the part where submitted_variant gets stored before everything else gets handled.

I would start investigating your server logs. If the submitted_variant from David's output and David's actual submitted variant are found at the same time in the server logs, you know it's a race condition. If the server really isn't so busy and there's time in between those two requests, it might also be some kind of caching. But then I don't know if you have implemented any caching at all or not.

[vidboda]

Hi both,

maybe related, here is another type of weird results (empty):

https://rest.variantvalidator.org/VariantValidator/variantvalidator/GRCh38/NM_018188.4:c.895-4G>A/all?content-type=application/json

{'flag': 'warning', 'metadata': {'variantvalidator_hgvs_version': '2.0.1', 'variantvalidator_version': '2.0.1.dev50+g4572981', 'vvdb_version': 'vvdb_2021_4', 'vvseqrepo_db': 'VV_SR_2021_2/master', 'vvta_version': 'vvta_2021_2'}, 'validation_warning_1': {'alt_genomic_loci': [], 'annotations': {}, 'gene_ids': {}, 'gene_symbol': '', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': '', 'tlr': ''}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': '', 'primary_assembly_loci': {}, 'reference_sequence_records': '', 'refseqgene_context_intronic_sequence': '', 'selected_assembly': 'GRCh38', 'submitted_variant': 'NM_001010867.3:c.*19G>A', 'transcript_description': '', 'validation_warnings': [], 'variant_exonic_positions': None}}

[i3hsInnovation]

@beboche @ifokkema . I have tweaked the server. The main thing I'm trying is using the worker-event MPM in apache.

Please let me know if you see any more of these events @beboche

[vidboda]

Hi both,
nice! I'll sure let you know as they occur on a daily basis.
cheers

[ifokkema]

Hi Pete, right now I'm getting lots of HTTP500s when using LRGs. Is this related? The same call with NCs work just fine.

[i3hsInnovation]

Might be that the databases are out of date. I'm making an update as we speak. Let me test locally and feed back. Will look at what is causing the error and send a better error message back and fix the error if the LRG is in the database, or when it is added in the next few days

[i3hsInnovation]

FYI, that means I think this is an unrelated issue, but thanks for the heads up.
What I'm looking for here is instances where you ask about variant A but get info about a different variant (B)

[ifokkema]

FYI, that means I think this is an unrelated issue, but thanks for the heads up. What I'm looking for here is instances where you ask about variant A but get info about a different variant (B)

Sure, but I was thinking that maybe it's caused by the updating of the server or so?

Now, the HTTP500 has disappeared and I'm getting a "LRG_199:g.1000del is an unsupported format: For assistance, submit variant description to https://rest.variantvalidator.org/". Should I create a new issue?

[Peter-J-Freeman]

Yes please. New issue for that one. It'll be a bug I need to kill quick