Sometimes VV returns random output that makes no sense - possible race condition

ifokkema commented 2 years ago

Describe the bug I believe @beboche mentioned this before, but perhaps that was over email and not as an issue because I can't find it.

I've been breaking my head for hours on why I get random fails of my tests and new code. After digging and digging and digging, I had to conclude VV just randomly gave me a different output, and I debugged the connection.

To Reproduce You need to be patient to reproduce this. I don't know why or when this happens - it seems random. I was calling the following URL repeatedly until I got JSON back which made no sense. https://rest.variantvalidator.org/VariantValidator/variantvalidator/GRCh37/NM_004006.3%3Ac.100del/all?content-type=application%2Fjson

Expected behavior I was expecting, and usually getting, the following output:

{
  "NM_004006.3:c.101del": {
    "alt_genomic_loci": [],
    "annotations": {
      "chromosome": "X",
      "db_xref": {
        "CCDS": "CCDS14233.1",
        "ensemblgene": null,
        "hgnc": "HGNC:2928",
        "ncbigene": "1756",
        "select": "MANE"
      },
      "ensembl_select": false,
      "mane_plus_clinical": false,
      "mane_select": true,
      "map": "Xp21.2-p21.1",
      "note": "dystrophin",
      "refseq_select": true,
      "variant": "DP427M"
    },
    "gene_ids": {
      "ccds_ids": [
        "CCDS14231",
        "CCDS14234",
        "CCDS48091",
        "CCDS55395",
        "CCDS14232",
        "CCDS75965",
        "CCDS14233",
        "CCDS55394"
      ],
      "ensembl_gene_id": "ENSG00000198947",
      "entrez_gene_id": "1756",
      "hgnc_id": "HGNC:2928",
      "omim_id": [
        "300377"
      ],
      "ucsc_id": "uc004dda.2"
    },
    "gene_symbol": "DMD",
    "genome_context_intronic_sequence": "",
    "hgvs_lrg_transcript_variant": "",
    "hgvs_lrg_variant": "",
    "hgvs_predicted_protein_consequence": {
      "lrg_slr": "",
      "lrg_tlr": "",
      "slr": "NP_003997.2:p.(K34Sfs*18)",
      "tlr": "NP_003997.2:p.(Lys34SerfsTer18)"
    },
    "hgvs_refseqgene_variant": "",
    "hgvs_transcript_variant": "NM_004006.3:c.101del",
    "primary_assembly_loci": {
      "grch37": {
        "hgvs_genomic_description": "NC_000023.10:g.32867931del",
        "vcf": {
          "alt": "C",
          "chr": "X",
          "pos": "32867929",
          "ref": "CT"
        }
      },
      "grch38": {
        "hgvs_genomic_description": "NC_000023.11:g.32849814del",
        "vcf": {
          "alt": "C",
          "chr": "X",
          "pos": "32849812",
          "ref": "CT"
        }
      },
      "hg19": {
        "hgvs_genomic_description": "NC_000023.10:g.32867931del",
        "vcf": {
          "alt": "C",
          "chr": "chrX",
          "pos": "32867929",
          "ref": "CT"
        }
      },
      "hg38": {
        "hgvs_genomic_description": "NC_000023.11:g.32849814del",
        "vcf": {
          "alt": "C",
          "chr": "chrX",
          "pos": "32849812",
          "ref": "CT"
        }
      }
    },
    "reference_sequence_records": {
      "protein": "https://www.ncbi.nlm.nih.gov/nuccore/NP_003997.2",
      "transcript": "https://www.ncbi.nlm.nih.gov/nuccore/NM_004006.3"
    },
    "refseqgene_context_intronic_sequence": "",
    "selected_assembly": "GRCh37",
    "submitted_variant": "NM_004006.3:c.100del",
    "transcript_description": "Homo sapiens dystrophin (DMD), transcript variant Dp427m, mRNA",
    "validation_warnings": [
      "NM_004006.3:c.100del automapped to NM_004006.3:c.101delA"
    ],
    "variant_exonic_positions": {
      "NC_000023.10": {
        "end_exon": "3",
        "start_exon": "3"
      },
      "NC_000023.11": {
        "end_exon": "3",
        "start_exon": "3"
      }
    }
  },
  "flag": "gene_variant",
  "metadata": {
    "variantvalidator_hgvs_version": "2.0.1",
    "variantvalidator_version": "2.1.1.dev34+gc25d2c9",
    "vvdb_version": "vvdb_2022_04",
    "vvseqrepo_db": "VV_SR_2022_02/master",
    "vvta_version": "vvta_2022_02"
  }
}

However, during debugging I suddenly got this:

{
  "flag": "warning",
  "metadata": {
    "variantvalidator_hgvs_version": "2.0.1",
    "variantvalidator_version": "2.1.1.dev34+gc25d2c9",
    "vvdb_version": "vvdb_2022_04",
    "vvseqrepo_db": "VV_SR_2022_02/master",
    "vvta_version": "vvta_2022_02"
  },
  "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": "hg19",
    "submitted_variant": "NM_007294.4:c.5092G>T",
    "transcript_description": "",
    "validation_warnings": [],
    "variant_exonic_positions": null
  }
}

The data is missing, the warning seems to point to nowhere, and the submitted_variant makes no sense. When I submit that variant, it actually seems to work fine. So this may be:

A race condition that not only selects output for a different variant but also breaks something inside VV that makes it return this almost-empty JSON.
Some other condition that perhaps returns some hard-coded output or some cached file from disk or so.

Could you please check your Apache logs if somebody submitted NM_007294.4:c.5092G>T just now? (note; you'd likely need to apply URL encoding while grepping, or grep parts of the variant) I submitted it once to confirm that the variant works. You'll be able to find my IP address by just grepping the logs for NM_004006.3%3Ac.100del that I submitted a LOT today. If a different IP submitted the c.5092G>T variant while I was busy with my c.100del variant, then we have concluded that a race condition exists in VV. It may not solve the error yet, but at least it gives an idea of where to start.

Peter-J-Freeman commented 2 years ago

server didn't restart. Should be ok now

ifokkema commented 2 years ago

Nope... still mostly HTTP 500 :cry:

ifokkema commented 2 years ago

I really think you'd better revert - since we need to conclude that the real cause is guesswork and the latest code causes severe issues worse than the original issues, it's best to revert completely and replan the update.

Peter-J-Freeman commented 2 years ago

Not really, I haven't actually added anything that should change the code. I need to debug.

Peter-J-Freeman commented 2 years ago

My bad, set bools and not strings! Altered, will adjust server now

Peter-J-Freeman commented 2 years ago

Back up. When I test locally the correct variable is not set

Peter-J-Freeman commented 2 years ago

OK, this is what I did.

Previously the line https://github.com/openvar/vv_hgvs/blob/master/vvhgvs/dataproviders/seqfetcher.py#L39 was hard coded to be check_same_thread=False

This in now configurable as you can see here https://github.com/openvar/vv_hgvs/blob/master/vvhgvs/dataproviders/seqfetcher.py#L39

I was just a numpty as you can see in these commits https://github.com/openvar/variantValidator/commit/47ee7400b9713ed519e89e962fc2ac87be77fe2b https://github.com/openvar/variantValidator/commit/53dc58b215f074c1cec8191e7f5e81baabc9ccce

If it's not working now, that will be really odd indeed.

ifokkema commented 2 years ago

It seems to work again! I'll restart my tester.

Peter-J-Freeman commented 2 years ago

Won't fix the race condition @ifokkema. I'm not sure I can since the SQLite connection is made in a 3rd party library, however I am gonna try

ifokkema commented 2 years ago

I'm glad you got it fixed! So far, my tests show it's working again. I'll let it run to see if it encounters the race condition again.

Are variant descriptions retrieved from SQLite? I thought SQLite was for reference sequences? You might be looking at multiple issues here. Since I now and then got to see variant descriptions submitted by others, and @beboche got to see output meant for others, I doubt this is just SQLite-related unless really everything moves through there, multiple times per request. Multiple times is also important because if SQLite were just used once every request to VV, we'd all be seeing the same thing - either only output meant for others or only errors with input from others, not both. Anyway, we can discuss this in more detail in our Tuesday call :wink:

Peter-J-Freeman commented 2 years ago

Nope, it's always the Sqlite database that reports errors and I think it is because SQLite has never been truly thread safe. I have now added a thread lock to the function that uses SQlite databases. Let's try it. All tests pass

Peter-J-Freeman commented 2 years ago

OK, running in thread lock protection mode

Can you

Confirm no errors when hammering
If OK, try create race conditions

Peter-J-Freeman commented 2 years ago

I doubt this is just SQLite-related unless really everything moves through there, multiple times per request

It does!

However, this is a good point. The return is at the variant level, so I wonder if I need to protect that too. In for a penny etc!!!!

ifokkema commented 2 years ago

Nope, it's always the Sqlite database that reports errors (...)

That's why I mentioned it could be multiple things - not every race condition will throw an error. It will simply replace data from one request with data from another request. So don't let the errors fool you :wink:

Either way, I've had some weird outputs, but most requests come back fine.

Peter-J-Freeman commented 2 years ago

Weird as in race like? Hope so. I think the SQLite stuff is now safer, but I think race will still be there

ifokkema commented 2 years ago

I'm not sure what to make of it... It's like the warning I got before, but then definitely my variant... but the warning is somehow also suddenly repeated...

{
  "flag": "warning",
  "metadata": {
    "variantvalidator_hgvs_version": "2.0.2.dev3+g035e049",
    "variantvalidator_version": "2.1.1.dev53+g1c75f94",
    "vvdb_version": "vvdb_2022_04",
    "vvseqrepo_db": "VV_SR_2022_02/master",
    "vvta_version": "vvta_2022_02"
  },
  "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": "GRCh37",
    "submitted_variant": "NM_004006.3:c.100del",
    "transcript_description": "",
    "validation_warnings": [
      "NM_004006.3:c.100del automapped to NM_004006.3:c.101delA"
    ],
    "variant_exonic_positions": null
  },
  "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": "GRCh37",
    "submitted_variant": "NM_004006.3:c.100del",
    "transcript_description": "",
    "validation_warnings": [
      "NM_004006.3:c.100del automapped to NM_004006.3:c.101delA"
    ],
    "variant_exonic_positions": null
  }
}

Another time I even got nine warnings in one output. The last warning was my variant, but the first eight warnings were from another variant, all the same variant, but different from my input.

{
  "flag": "warning",
  "metadata": {
    "variantvalidator_hgvs_version": "2.0.2.dev3+g035e049",
    "variantvalidator_version": "2.1.1.dev53+g1c75f94",
    "vvdb_version": "vvdb_2022_04",
    "vvseqrepo_db": "VV_SR_2022_02/master",
    "vvta_version": "vvta_2022_02"
  },
  "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_000002.12:g.47805070dup",
    "transcript_description": "",
    "validation_warnings": [],
    "variant_exonic_positions": null
  },
(...)
  "validation_warning_8": {
    "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_000002.12:g.47805070dup",
    "transcript_description": "",
    "validation_warnings": [],
    "variant_exonic_positions": null
  },
  "validation_warning_9": {
    "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": "GRCh37",
    "submitted_variant": "NM_004006.3:c.100del",
    "transcript_description": "",
    "validation_warnings": [
      "NM_004006.3:c.100del automapped to NM_004006.3:c.101delA"
    ],
    "variant_exonic_positions": null
  }
}

Peter-J-Freeman commented 2 years ago

Right, I think what I might try next is to add thread locking to the REST API endpoints. Will try this tomorrow though. It seems like the logical place to start

vidboda commented 2 years ago

Hi guys, I was out of the lab on last Thursday and Friday - I've noticed the ~2hrs VV downtime (which was translated for me into ~100 errors emails). However, no race conditions noted since. @Peter-J-Freeman you wrote it was not fixed yet but so far so good. Maybe also the guy that validated every possible position of his transcript has ended, which may help. I'll let you know if sthg occurs.

ifokkema commented 2 years ago

I still had issues on the 16th, but then I had to kill the script as we had a planned power outage last weekend. I'll turn it on again to verify if I still see them now.

vidboda commented 2 years ago

Also @Peter-J-Freeman on this comment you can see IP addresses maybe you should erase it: https://github.com/openvar/variantValidator/issues/421#issuecomment-1246734094

ifokkema commented 2 years ago

Also @Peter-J-Freeman on this comment you can see IP addresses maybe you should erase it: #421 (comment)

I second that - it should indeed be removed.

I still had issues on the 16th, but then I had to kill the script as we had a planned power outage last weekend. I'll turn it on again to verify if I still see them now.

I've confirmed that I'm still getting race conditions... so it's still there :wink:

Peter-J-Freeman commented 2 years ago

I've confirmed that I'm still getting race conditions... so it's still there 😉

Yeah, this is expected. Will likely be next week before I have time to try again

vidboda commented 2 years ago

Hi guys the race condition just occured twice in 10 minutes, both times with a reported submitted variant different from the real submitted variant (which we could call the 'classical' case)

Peter-J-Freeman commented 2 years ago

Moving this to the new API Repo https://github.com/openvar/VariantsInJournals/issues/5

lcoutos commented 1 year ago

Hi, I come back with more details and few tests with batch requests and waiting few seconds between two requests. Sleeping time does not prevent a bad response, even 10 or 20 seconds. Most of the time, I can have entire series without any bug, and few hour later, all the requests returns the response of someone else.

For batch requests, three types of errors: I can retrieve a completely different response, as follow:

## URL #####################
https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg19/NM_000321.2:c.1994T>C|NM_004440.3:c.1378G>T|NM_000720.3:c.6360G>C|NM_004440.3:c.1909C>T|NM_003205.3:c.1196G>A|NM_004326.3:c.1355C>A|NM_001320135.1:c.1852T>A|NM_020399.3:c.56C>T|NM_006015.4:c.2615T>C|NM_016320.4:c.1288T>A|NM_004721.4:c.104G>A|NM_078467.2:c.350G>A|NM_001042771.2:c.632A>T|NM_002456.5:c.547G>A|NM_020732.3:c.1494C>G|NM_001332.3:c.238C>G/all?content-type=application%2Fjson

## OK #########################
[]

## Not sent #########################
['19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT']

## Not received #########################
['NM_000321.2:c.1994T>C', 'NM_004440.3:c.1378G>T', 'NM_000720.3:c.6360G>C', 'NM_004440.3:c.1909C>T', 'NM_003205.3:c.1196G>A', 'NM_004326.3:c.1355C>A', 'NM_001320135.1:c.1852T>A', 'NM_020399.3:c.56C>T', 'NM_006015.4:c.2615T>C', 'NM_016320.4:c.1288T>A', 'NM_004721.4:c.104G>A', 'NM_078467.2:c.350G>A', 'NM_001042771.2:c.632A>T', 'NM_002456.5:c.547G>A', 'NM_020732.3:c.1494C>G', 'NM_001332.3:c.238C>G']

## Full Response #########################
{'NM_004343.3:c.1102_1139delinsCTTT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '19', 'db_xref': {'CCDS': 'CCDS12288.1', 'ensemblgene': None, 'hgnc': 'HGNC:1455', 'ncbigene': '811', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '19p13.13', 'note': 'calreticulin', 'refseq_select': True, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS12288'], 'ensembl_gene_id': 'ENSG00000179218', 'entrez_gene_id': '811', 'hgnc_id': 'HGNC:1455', 'omim_id': ['109091'], 'ucsc_id': 'uc002mvu.3'}, 'gene_symbol': 'CALR', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_828t1:c.1102_1139delinsCTTT', 'hgvs_lrg_variant': 'LRG_828:g.10162_10199delinsCTTT', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_828p1:p.(K368Lfs*51)', 'lrg_tlr': 'LRG_828p1:p.(Lys368LeufsTer51)', 'slr': 'NP_004334.1:p.(K368Lfs*51)', 'tlr': 'NP_004334.1:p.(Lys368LeufsTer51)'}, 'hgvs_refseqgene_variant': 'NG_029662.1:g.10162_10199delinsCTTT', 'hgvs_transcript_variant': 'NM_004343.3:c.1102_1139delinsCTTT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'grch38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg19': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_828.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004334.1', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_029662.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004343.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', 'transcript_description': 'Homo sapiens calreticulin (CALR), mRNA', 'validation_warnings': ['NC_000019.9:g.13054575AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA>CTTT automapped to NC_000019.9:g.13054575_13054612delinsCTTT', 'A more recent version of the selected reference sequence NM_004343.3 is available (NM_004343.4): NM_004343.4:c.1102_1139delinsCTTT MUST be fully validated prior to use in reports: select_variants=NM_004343.4:c.1102_1139delinsCTTT'], 'variant_exonic_positions': {'NC_000019.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000019.9': {'end_exon': '9', 'start_exon': '9'}, 'NG_029662.1': {'end_exon': '9', 'start_exon': '9'}}}, 'NM_004343.4:c.1102_1139delinsCTTT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '19', 'db_xref': {'CCDS': 'CCDS12288.1', 'ensemblgene': None, 'hgnc': 'HGNC:1455', 'ncbigene': '811', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '19p13.13', 'note': 'calreticulin', 'refseq_select': True, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS12288'], 'ensembl_gene_id': 'ENSG00000179218', 'entrez_gene_id': '811', 'hgnc_id': 'HGNC:1455', 'omim_id': ['109091'], 'ucsc_id': 'uc002mvu.3'}, 'gene_symbol': 'CALR', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_828p1:p.(K368Lfs*51)', 'lrg_tlr': 'LRG_828p1:p.(Lys368LeufsTer51)', 'slr': 'NP_004334.1:p.(K368Lfs*51)', 'tlr': 'NP_004334.1:p.(Lys368LeufsTer51)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_004343.4:c.1102_1139delinsCTTT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'grch38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg19': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004334.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004343.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', 'transcript_description': 'Homo sapiens calreticulin (CALR), mRNA', 'validation_warnings': ['NC_000019.9:g.13054575AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA>CTTT automapped to NC_000019.9:g.13054575_13054612delinsCTTT'], 'variant_exonic_positions': {'NC_000019.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000019.9': {'end_exon': '9', 'start_exon': '9'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

Or I can have my variants and also variants I haven’t sent:

## URL #####################
https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg19/NM_133170.3:c.3982G>T|NM_022768.4:c.623C>G|NM_001190326.1:c.1988G>A|NM_020975.4:c.166C>A|NM_020311.2:c.410G>A|NM_007166.3:c.1394A>G|NM_016569.3:c.112C>A|NM_001109754.3:c.3167C>T/all?content-type=application%2Fjson

## OK #########################
['NM_133170.3:c.3982G>T', 'NM_022768.4:c.623C>G', 'NM_001190326.1:c.1988G>A', 'NM_020975.4:c.166C>A', 'NM_020311.2:c.410G>A', 'NM_007166.3:c.1394A>G', 'NM_016569.3:c.112C>A', 'NM_001109754.3:c.3167C>T']

## Not sent ######################### 
['13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC']

## Not received #########################
[]

## Full Response #########################
{'NM_001109754.3:c.3167C>T': {'alt_genomic_loci': [], 'annotations': {'chromosome': '12', 'db_xref': {'CCDS': 'CCDS44943.1', 'ensemblgene': None, 'hgnc': 'HGNC:9665', 'ncbigene': '5787', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '12q15', 'note': 'protein tyrosine phosphatase receptor type B', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS44943', 'CCDS55846', 'CCDS44944', 'CCDS81713', 'CCDS55845'], 'ensembl_gene_id': 'ENSG00000127329', 'entrez_gene_id': '5787', 'hgnc_id': 'HGNC:9665', 'omim_id': ['176882'], 'ucsc_id': 'uc001swc.6'}, 'gene_symbol': 'PTPRB', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_001103224.1:p.(T1056I)', 'tlr': 'NP_001103224.1:p.(Thr1056Ile)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_001109754.3:c.3167C>T', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000012.11:g.70965009G>A', 'vcf': {'alt': 'A', 'chr': '12', 'pos': '70965009', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000012.12:g.70571229G>A', 'vcf': {'alt': 'A', 'chr': '12', 'pos': '70571229', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000012.11:g.70965009G>A', 'vcf': {'alt': 'A', 'chr': 'chr12', 'pos': '70965009', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000012.12:g.70571229G>A', 'vcf': {'alt': 'A', 'chr': 'chr12', 'pos': '70571229', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_001103224.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_001109754.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_001109754.3:c.3167C>T', 'transcript_description': 'Homo sapiens protein tyrosine phosphatase receptor type B (PTPRB), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001109754.3 is available (NM_001109754.4): NM_001109754.4:c.3167C>T MUST be fully validated prior to use in reports: select_variants=NM_001109754.4:c.3167C>T'], 'variant_exonic_positions': {'NC_000012.11': {'end_exon': '13', 'start_exon': '13'}, 'NC_000012.12': {'end_exon': '13', 'start_exon': '13'}}}, 'NM_001190326.1:c.1988G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '22', 'db_xref': {'CCDS': 'CCDS54501.1', 'ensemblgene': None, 'hgnc': 'HGNC:2847', 'ncbigene': '54487', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '22q11.21', 'note': 'DGCR8 microprocessor complex subunit', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS54501', 'CCDS13773'], 'ensembl_gene_id': 'ENSG00000128191', 'entrez_gene_id': '54487', 'hgnc_id': 'HGNC:2847', 'omim_id': ['609030'], 'ucsc_id': 'uc002zri.4'}, 'gene_symbol': 'DGCR8', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_001177255.1:p.(R663H)', 'tlr': 'NP_001177255.1:p.(Arg663His)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_001190326.1:c.1988G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000022.10:g.20094884G>A', 'vcf': {'alt': 'A', 'chr': '22', 'pos': '20094884', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000022.11:g.20107361G>A', 'vcf': {'alt': 'A', 'chr': '22', 'pos': '20107361', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000022.10:g.20094884G>A', 'vcf': {'alt': 'A', 'chr': 'chr22', 'pos': '20094884', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000022.11:g.20107361G>A', 'vcf': {'alt': 'A', 'chr': 'chr22', 'pos': '20107361', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_001177255.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_001190326.1'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_001190326.1:c.1988G>A', 'transcript_description': 'Homo sapiens DGCR8 microprocessor complex subunit (DGCR8), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001190326.1 is available (NM_001190326.2): NM_001190326.2:c.1988G>A MUST be fully validated prior to use in reports: select_variants=NM_001190326.2:c.1988G>A'], 'variant_exonic_positions': {'NC_000022.10': {'end_exon': '11', 'start_exon': '11'}, 'NC_000022.11': {'end_exon': '11', 'start_exon': '11'}}}, 'NM_004119.2:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': 'CCDS31953.1', 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_457t1:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_lrg_variant': 'LRG_457:g.71471_71476delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_457p1:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'lrg_tlr': 'LRG_457p1:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)', 'slr': 'NP_004110.2:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'tlr': 'NP_004110.2:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)'}, 'hgvs_refseqgene_variant': 'NG_007066.1:g.71471_71476delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_transcript_variant': 'NM_004119.2:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_457.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004110.2', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_007066.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004119.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related tyrosine kinase 3 (FLT3), transcript variant 1, mRNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'A more recent version of the selected reference sequence NM_004119.2 is available (NM_004119.3): NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT MUST be fully validated prior to use in reports: select_variants=NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}, 'NG_007066.1': {'end_exon': '14', 'start_exon': '14'}}}, 'NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': 'CCDS31953.1', 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_457p1:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'lrg_tlr': 'LRG_457p1:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)', 'slr': 'NP_004110.2:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'tlr': 'NP_004110.2:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos':
 '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004110.2', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004119.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related receptor tyrosine kinase 3 (FLT3), transcript variant 1, mRNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'NM_007166.3:c.1394A>G': {'alt_genomic_loci': [], 'annotations': {'chromosome': '11', 'db_xref': {'CCDS': 'CCDS8272.1', 'ensemblgene': None, 'hgnc': 'HGNC:15514', 'ncbigene': '8301', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '11q14.2', 'note': 'phosphatidylinositol binding clathrin assembly protein', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS55783', 'CCDS55784', 'CCDS8272', 'CCDS31653'], 'ensembl_gene_id': 'ENSG00000073921', 'entrez_gene_id': '8301', 'hgnc_id': 'HGNC:15514', 'omim_id': ['603025'], 'ucsc_id': 'uc001pbm.4'}, 'gene_symbol': 'PICALM', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_009097.2:p.(H465R)', 'tlr': 'NP_009097.2:p.(His465Arg)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_007166.3:c.1394A>G', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000011.9:g.85701307T>C', 'vcf': {'alt': 'C', 'chr': '11', 'pos': '85701307', 'ref': 'T'}}, 'grch38': {'hgvs_genomic_description': 'NC_000011.10:g.85990264T>C', 'vcf': {'alt': 'C', 'chr': '11', 'pos': '85990264', 'ref': 'T'}}, 'hg19': {'hgvs_genomic_description': 'NC_000011.9:g.85701307T>C', 'vcf': {'alt': 'C', 'chr': 'chr11', 'pos': '85701307', 'ref': 'T'}}, 'hg38': {'hgvs_genomic_description': 'NC_000011.10:g.85990264T>C', 'vcf': {'alt': 'C', 'chr': 'chr11', 'pos': '85990264', 'ref': 'T'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_009097.2', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_007166.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_007166.3:c.1394A>G', 'transcript_description': 'Homo sapiens phosphatidylinositol binding clathrin assembly protein (PICALM), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_007166.3 is available (NM_007166.4): NM_007166.4:c.1394A>G MUST be fully validated prior to use in reports: select_variants=NM_007166.4:c.1394A>G'], 'variant_exonic_positions': {'NC_000011.10': {'end_exon': '13', 'start_exon': '13'}, 'NC_000011.9': {'end_exon': '13', 'start_exon': '13'}}}, 'NM_016569.3:c.112C>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '12', 'db_xref': {'CCDS': 'CCDS9176.1', 'ensemblgene': None, 'hgnc': 'HGNC:11602', 'ncbigene': '6926', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '12q24.21', 'note': 'T-box transcription factor 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS9176', 'CCDS9175'], 'ensembl_gene_id': 'ENSG00000135111', 'entrez_gene_id': '6926', 'hgnc_id': 'HGNC:11602', 'omim_id': ['601621'], 'ucsc_id': 'uc001tvt.2'}, 'gene_symbol': 'TBX3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_057653.3:p.(P38T)', 'tlr': 'NP_057653.3:p.(Pro38Thr)'}, 'hgvs_refseqgene_variant': 'NG_008315.1:g.6076C>A', 'hgvs_transcript_variant': 'NM_016569.3:c.112C>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000012.11:g.115120894G>T', 'vcf': {'alt': 'T', 'chr': '12', 'pos': '115120894', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000012.12:g.114683089G>T', 'vcf': {'alt': 'T', 'chr': '12', 'pos': '114683089', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000012.11:g.115120894G>T', 'vcf': {'alt': 'T', 'chr': 'chr12', 'pos': '115120894', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000012.12:g.114683089G>T', 'vcf': {'alt': 'T', 'chr': 'chr12', 'pos': '114683089', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_057653.3', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_008315.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_016569.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_016569.3:c.112C>A', 'transcript_description': 'Homo sapiens T-box 3 (TBX3), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_016569.3 is available (NM_016569.4): NM_016569.4:c.112C>A MUST be fully validated prior to use in reports: select_variants=NM_016569.4:c.112C>A'], 'variant_exonic_positions': {'NC_000012.11': {'end_exon': '1', 'start_exon': '1'}, 'NC_000012.12': {'end_exon': '1', 'start_exon': '1'}, 'NG_008315.1': {'end_exon': '1', 'start_exon': '1'}}}, 'NM_020311.2:c.410G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '2', 'db_xref': {'CCDS': 'CCDS2516.1', 'ensemblgene': None, 'hgnc': 'HGNC:23692', 'ncbigene': '57007', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '2q37.3', 'note': 'atypical chemokine receptor 3', 'refseq_select': False, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS2516'], 'ensembl_gene_id': 'ENSG00000144476', 'entrez_gene_id': '57007', 'hgnc_id': 'HGNC:23692', 'omim_id': ['610376'], 'ucsc_id': ''}, 'gene_symbol': 'ACKR3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_064707.1:p.(C137Y)', 'tlr': 'NP_064707.1:p.(Cys137Tyr)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_020311.2:c.410G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000002.11:g.237489518G>A', 'vcf': {'alt': 'A', 'chr': '2', 'pos': '237489518', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000002.12:g.236580875G>A', 'vcf': {'alt': 'A', 'chr': '2', 'pos': '236580875', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000002.11:g.237489518G>A', 'vcf': {'alt': 'A', 'chr': 'chr2', 'pos': '237489518', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000002.12:g.236580875G>A', 'vcf': {'alt': 'A', 'chr': 'chr2', 'pos': '236580875', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_064707.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_020311.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_020311.2:c.410G>A', 'transcript_description': 'Homo sapiens atypical chemokine receptor 3 (ACKR3), mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_020311.2 is available (NM_020311.3): NM_020311.3:c.410G>A MUST be fully validated prior to use in reports: select_variants=NM_020311.3:c.410G>A'], 'variant_exonic_positions': {'NC_000002.11': {'end_exon': '2', 'start_exon': '2'}, 'NC_000002.12': {'end_exon': '2', 'start_exon': '2'}}}, 'NM_020975.4:c.166C>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '10', 'db_xref': {'CCDS': 'CCDS7200.1', 'ensemblgene': None, 'hgnc': 'HGNC:9967', 'ncbigene': '5979', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '10q11.21', 'note': 'ret proto-oncogene', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS7200', 'CCDS53525'], 'ensembl_gene_id': 'ENSG00000165731', 'entrez_gene_id': '5979', 'hgnc_id': 'HGNC:9967', 'omim_id': ['164761'], 'ucsc_id': 'uc001jal.4'}, 'gene_symbol': 'RET', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_518t1:c.166C>A', 'hgvs_lrg_variant': 'LRG_518:g.28483C>A', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_518p1:p.(L56M)', 'lrg_tlr': 'LRG_518p1:p.(Leu56Met)', 'slr': 'NP_066124.1:p.(L56M)', 'tlr': 'NP_066124.1:p.(Leu56Met)'}, 'hgvs_refseqgene_variant': 'NG_007489.1:g.28483C>A', 'hgvs_transcript_variant': 'NM_020975.4:c.166C>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000010.10:g.43595999C>A', 'vcf': {'alt': 'A', 'chr': '10', 'pos': '43595999', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000010.11:g.43100551C>A', 'vcf': {'alt': 'A', 'chr': '10', 'pos': '43100551', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000010.10:g.43595999C>A',
 'vcf': {'alt': 'A', 'chr': 'chr10', 'pos': '43595999', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000010.11:g.43100551C>A', 'vcf': {'alt': 'A', 'chr': 'chr10', 'pos': '43100551', 'ref': 'C'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_518.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_066124.1', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_007489.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_020975.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_020975.4:c.166C>A', 'transcript_description': 'Homo sapiens ret proto-oncogene (RET), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_020975.4 is available (NM_020975.6): NM_020975.6:c.166C>A MUST be fully validated prior to use in reports: select_variants=NM_020975.6:c.166C>A'], 'variant_exonic_positions': {'NC_000010.10': {'end_exon': '2', 'start_exon': '2'}, 'NC_000010.11': {'end_exon': '2', 'start_exon': '2'}, 'NG_007489.1': {'end_exon': '2', 'start_exon': '2'}}}, 'NM_022768.4:c.623C>G': {'alt_genomic_loci': [], 'annotations': {'chromosome': '1', 'db_xref': {'CCDS': 'CCDS822.1', 'ensemblgene': None, 'hgnc': 'HGNC:14959', 'ncbigene': '64783', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '1p13.3', 'note': 'RNA binding motif protein 15', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS59198', 'CCDS822'], 'ensembl_gene_id': 'ENSG00000162775', 'entrez_gene_id': '64783', 'hgnc_id': 'HGNC:14959', 'omim_id': ['606077'], 'ucsc_id': 'uc021orn.2'}, 'gene_symbol': 'RBM15', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_073605.4:p.(S208W)', 'tlr': 'NP_073605.4:p.(Ser208Trp)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_022768.4:c.623C>G', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000001.10:g.110882650C>G', 'vcf': {'alt': 'G', 'chr': '1', 'pos': '110882650', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000001.11:g.110340028C>G', 'vcf': {'alt': 'G', 'chr': '1', 'pos': '110340028', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000001.10:g.110882650C>G', 'vcf': {'alt': 'G', 'chr': 'chr1', 'pos': '110882650', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000001.11:g.110340028C>G', 'vcf': {'alt': 'G', 'chr': 'chr1', 'pos': '110340028', 'ref': 'C'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_073605.4', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_022768.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_022768.4:c.623C>G', 'transcript_description': 'Homo sapiens RNA binding motif protein 15 (RBM15), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_022768.4 is available (NM_022768.5): NM_022768.5:c.623C>G MUST be fully validated prior to use in reports: select_variants=NM_022768.5:c.623C>G'], 'variant_exonic_positions': {'NC_000001.10': {'end_exon': '1', 'start_exon': '1'}, 'NC_000001.11': {'end_exon': '1', 'start_exon': '1'}}}, 'NM_133170.3:c.3982G>T': {'alt_genomic_loci': [], 'annotations': {'chromosome': '20', 'db_xref': {'CCDS': 'CCDS68127.1', 'ensemblgene': None, 'hgnc': 'HGNC:9682', 'ncbigene': '11122', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '20q12-q13.11', 'note': 'protein tyrosine phosphatase receptor type T', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS42874', 'CCDS68127'], 'ensembl_gene_id': 'ENSG00000196090', 'entrez_gene_id': '11122', 'hgnc_id': 'HGNC:9682', 'omim_id': ['608712'], 'ucsc_id': 'uc061xcb.1'}, 'gene_symbol': 'PTPRT', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_573400.3:p.(D1328Y)', 'tlr': 'NP_573400.3:p.(Asp1328Tyr)'}, 'hgvs_refseqgene_variant': 'NG_033880.1:g.1109143G>T', 'hgvs_transcript_variant': 'NM_133170.3:c.3982G>T', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000020.10:g.40714415C>A', 'vcf': {'alt': 'A', 'chr': '20', 'pos': '40714415', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000020.11:g.42085775C>A', 'vcf': {'alt': 'A', 'chr': '20', 'pos': '42085775', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000020.10:g.40714415C>A', 'vcf': {'alt': 'A', 'chr': 'chr20', 'pos': '40714415', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000020.11:g.42085775C>A', 'vcf': {'alt': 'A', 'chr': 'chr20', 'pos': '42085775', 'ref': 'C'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_573400.3', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_033880.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_133170.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_133170.3:c.3982G>T', 'transcript_description': 'Homo sapiens protein tyrosine phosphatase receptor type T (PTPRT), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_133170.3 is available (NM_133170.4): NM_133170.4:c.3982G>T MUST be fully validated prior to use in reports: select_variants=NM_133170.4:c.3982G>T'], 'variant_exonic_positions': {'NC_000020.10': {'end_exon': '29', 'start_exon': '29'}, 'NC_000020.11': {'end_exon': '29', 'start_exon': '29'}, 'NG_033880.1': {'end_exon': '29', 'start_exon': '29'}}}, 'NR_130706.1:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': None, 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', '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': 'NR_130706.1:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NR_130706.1'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related tyrosine kinase 3 (FLT3), transcript variant 2, non-coding RNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'A more recent version of the selected reference sequence NR_130706.1 is available (NR_130706.2): NR_130706.2:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT MUST be fully validated prior to use in reports: select_variants=NR_130706.2:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'NR_130706.2:n.1887_1892delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': None, 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', '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': 'NR_130706.2:n.1887_1892delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci':
 {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NR_130706.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related receptor tyrosine kinase 3 (FLT3), transcript variant 2, non-coding RNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

The second situation could explain the third one, the empty response:

{'flag': 'empty_result', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

For the moment, I have no cases of missing variants in a partially good response, but it could just be luck. I hope this helps.

Peter-J-Freeman commented 1 year ago

Hi,

Thanks for the clarification. We are aware of these issues. The server is being used much more these days than a year ago and we have discovered that we are experiencing RACE conditions that occasionally cause this issue. We are currently working on the problem but it is a tricky one to pin down.

We are moving to new servers and new infrastructure in the coming months, so hopefully this will resolve.

Please feel free to keep in touch and let us know when this happens. Any particular times of day etc. It may help us to pin the issue down.

Many thanks

Dr Peter Freeman Lecturer in Healthcare sciences (Clinical bioinformatics, genomics) Division of Informatics, Imaging & Data Science Faculty of Biology, Medicine and Health | The University of Manchester G.725 | Stopford Building | Oxford Road | Manchester | M13 9PT Tel: +44(0) 161 275 5731 email: @.**@.> web: Peter Freemanhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.research.manchester.ac.uk%2Fportal%2Fpeter.j.freeman.html&data=05%7C01%7Crebecca.hames%40leicester.ac.uk%7C3ed7a3ebecb64fc30b2e08dabd8ae1e2%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C638030701461441392%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tN9K1dNirGZxpNZqEb%2BuZT8dpke%2BKNMsjknoDtGYfns%3D&reserved=0

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From: lcoutos @.> Date: Tuesday, 7 February 2023 at 15:18 To: openvar/variantValidator @.> Cc: Peter Freeman @.>, State change @.> Subject: Re: [openvar/variantValidator] Sometimes VV returns random output that makes no sense - possible race condition (Issue #421)

Hi, I come back with more details and few tests with batch requests and waiting few seconds between two requests. Sleeping time does not prevent a bad response, even 10 or 20 seconds. Most of the time, I can have entire series without any bug, and few hour later, all the requests returns the response of someone else.

For batch requests, three types of errors: I can retrieve a completely different response, as follow:

URL

OK

[]

Not sent

['19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT']

Not received

['NM_000321.2:c.1994T>C', 'NM_004440.3:c.1378G>T', 'NM_000720.3:c.6360G>C', 'NM_004440.3:c.1909C>T', 'NM_003205.3:c.1196G>A', 'NM_004326.3:c.1355C>A', 'NM_001320135.1:c.1852T>A', 'NM_020399.3:c.56C>T', 'NM_006015.4:c.2615T>C', 'NM_016320.4:c.1288T>A', 'NM_004721.4:c.104G>A', 'NM_078467.2:c.350G>A', 'NM_001042771.2:c.632A>T', 'NM_002456.5:c.547G>A', 'NM_020732.3:c.1494C>G', 'NM_001332.3:c.238C>G']

Full Response

{'NM_004343.3:c.1102_1139delinsCTTT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '19', 'db_xref': {'CCDS': 'CCDS12288.1', 'ensemblgene': None, 'hgnc': 'HGNC:1455', 'ncbigene': '811', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '19p13.13', 'note': 'calreticulin', 'refseq_select': True, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS12288'], 'ensembl_gene_id': 'ENSG00000179218', 'entrez_gene_id': '811', 'hgnc_id': 'HGNC:1455', 'omim_id': ['109091'], 'ucsc_id': 'uc002mvu.3'}, 'gene_symbol': 'CALR', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_828t1:c.1102_1139delinsCTTT', 'hgvs_lrg_variant': 'LRG_828:g.10162_10199delinsCTTT', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_828p1:p.(K368Lfs51)', 'lrg_tlr': 'LRG_828p1:p.(Lys368LeufsTer51)', 'slr': 'NP_004334.1:p.(K368Lfs51)', 'tlr': 'NP_004334.1:p.(Lys368LeufsTer51)'}, 'hgvs_refseqgene_variant': 'NG_029662.1:g.10162_10199delinsCTTT', 'hgvs_transcript_variant': 'NM_004343.3:c.1102_1139delinsCTTT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'grch38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg19': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_828.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004334.1', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_029662.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004343.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', 'transcript_description': 'Homo sapiens calreticulin (CALR), mRNA', 'validation_warnings': ['NC_000019.9:g.13054575AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA>CTTT automapped to NC_000019.9:g.13054575_13054612delinsCTTT', 'A more recent version of the selected reference sequence NM_004343.3 is available (NM_004343.4): NM_004343.4:c.1102_1139delinsCTTT MUST be fully validated prior to use in reports: select_variants=NM_004343.4:c.1102_1139delinsCTTT'], 'variant_exonic_positions': {'NC_000019.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000019.9': {'end_exon': '9', 'start_exon': '9'}, 'NG_029662.1': {'end_exon': '9', 'start_exon': '9'}}}, 'NM_004343.4:c.1102_1139delinsCTTT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '19', 'db_xref': {'CCDS': 'CCDS12288.1', 'ensemblgene': None, 'hgnc': 'HGNC:1455', 'ncbigene': '811', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '19p13.13', 'note': 'calreticulin', 'refseq_select': True, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS12288'], 'ensembl_gene_id': 'ENSG00000179218', 'entrez_gene_id': '811', 'hgnc_id': 'HGNC:1455', 'omim_id': ['109091'], 'ucsc_id': 'uc002mvu.3'}, 'gene_symbol': 'CALR', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_828p1:p.(K368Lfs51)', 'lrg_tlr': 'LRG_828p1:p.(Lys368LeufsTer51)', 'slr': 'NP_004334.1:p.(K368Lfs51)', 'tlr': 'NP_004334.1:p.(Lys368LeufsTer51)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_004343.4:c.1102_1139delinsCTTT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'grch38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': '19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg19': {'hgvs_genomic_description': 'NC_000019.9:g.13054575_13054612delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '13054575', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}, 'hg38': {'hgvs_genomic_description': 'NC_000019.10:g.12943761_12943798delinsCTTT', 'vcf': {'alt': 'CTTT', 'chr': 'chr19', 'pos': '12943761', 'ref': 'AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004334.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004343.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '19:13054575:AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA:CTTT', 'transcript_description': 'Homo sapiens calreticulin (CALR), mRNA', 'validation_warnings': ['NC_000019.9:g.13054575AAGGAGGAGGAAGAAGACAAGAAACGCAAAGAGGAGGA>CTTT automapped to NC_000019.9:g.13054575_13054612delinsCTTT'], 'variant_exonic_positions': {'NC_000019.10': {'end_exon': '9', 'start_exon': '9'}, 'NC_000019.9': {'end_exon': '9', 'start_exon': '9'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

Or I can have my variants and also variants and haven’t sent:

URL

OK

['NM_133170.3:c.3982G>T', 'NM_022768.4:c.623C>G', 'NM_001190326.1:c.1988G>A', 'NM_020975.4:c.166C>A', 'NM_020311.2:c.410G>A', 'NM_007166.3:c.1394A>G', 'NM_016569.3:c.112C>A', 'NM_001109754.3:c.3167C>T']

Not sent

['13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC']

Not received

[]

Full Response

{'NM_001109754.3:c.3167C>T': {'alt_genomic_loci': [], 'annotations': {'chromosome': '12', 'db_xref': {'CCDS': 'CCDS44943.1', 'ensemblgene': None, 'hgnc': 'HGNC:9665', 'ncbigene': '5787', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '12q15', 'note': 'protein tyrosine phosphatase receptor type B', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS44943', 'CCDS55846', 'CCDS44944', 'CCDS81713', 'CCDS55845'], 'ensembl_gene_id': 'ENSG00000127329', 'entrez_gene_id': '5787', 'hgnc_id': 'HGNC:9665', 'omim_id': ['176882'], 'ucsc_id': 'uc001swc.6'}, 'gene_symbol': 'PTPRB', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_001103224.1:p.(T1056I)', 'tlr': 'NP_001103224.1:p.(Thr1056Ile)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_001109754.3:c.3167C>T', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000012.11:g.70965009G>A', 'vcf': {'alt': 'A', 'chr': '12', 'pos': '70965009', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000012.12:g.70571229G>A', 'vcf': {'alt': 'A', 'chr': '12', 'pos': '70571229', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000012.11:g.70965009G>A', 'vcf': {'alt': 'A', 'chr': 'chr12', 'pos': '70965009', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000012.12:g.70571229G>A', 'vcf': {'alt': 'A', 'chr': 'chr12', 'pos': '70571229', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_001103224.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_001109754.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_001109754.3:c.3167C>T', 'transcript_description': 'Homo sapiens protein tyrosine phosphatase receptor type B (PTPRB), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001109754.3 is available (NM_001109754.4): NM_001109754.4:c.3167C>T MUST be fully validated prior to use in reports: select_variants=NM_001109754.4:c.3167C>T'], 'variant_exonic_positions': {'NC_000012.11': {'end_exon': '13', 'start_exon': '13'}, 'NC_000012.12': {'end_exon': '13', 'start_exon': '13'}}}, 'NM_001190326.1:c.1988G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '22', 'db_xref': {'CCDS': 'CCDS54501.1', 'ensemblgene': None, 'hgnc': 'HGNC:2847', 'ncbigene': '54487', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '22q11.21', 'note': 'DGCR8 microprocessor complex subunit', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS54501', 'CCDS13773'], 'ensembl_gene_id': 'ENSG00000128191', 'entrez_gene_id': '54487', 'hgnc_id': 'HGNC:2847', 'omim_id': ['609030'], 'ucsc_id': 'uc002zri.4'}, 'gene_symbol': 'DGCR8', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_001177255.1:p.(R663H)', 'tlr': 'NP_001177255.1:p.(Arg663His)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_001190326.1:c.1988G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000022.10:g.20094884G>A', 'vcf': {'alt': 'A', 'chr': '22', 'pos': '20094884', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000022.11:g.20107361G>A', 'vcf': {'alt': 'A', 'chr': '22', 'pos': '20107361', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000022.10:g.20094884G>A', 'vcf': {'alt': 'A', 'chr': 'chr22', 'pos': '20094884', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000022.11:g.20107361G>A', 'vcf': {'alt': 'A', 'chr': 'chr22', 'pos': '20107361', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_001177255.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_001190326.1'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_001190326.1:c.1988G>A', 'transcript_description': 'Homo sapiens DGCR8 microprocessor complex subunit (DGCR8), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_001190326.1 is available (NM_001190326.2): NM_001190326.2:c.1988G>A MUST be fully validated prior to use in reports: select_variants=NM_001190326.2:c.1988G>A'], 'variant_exonic_positions': {'NC_000022.10': {'end_exon': '11', 'start_exon': '11'}, 'NC_000022.11': {'end_exon': '11', 'start_exon': '11'}}}, 'NM_004119.2:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': 'CCDS31953.1', 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': 'RefSeq'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_457t1:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_lrg_variant': 'LRG_457:g.71471_71476delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_457p1:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'lrg_tlr': 'LRG_457p1:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)', 'slr': 'NP_004110.2:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'tlr': 'NP_004110.2:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)'}, 'hgvs_refseqgene_variant': 'NG_007066.1:g.71471_71476delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'hgvs_transcript_variant': 'NM_004119.2:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_457.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004110.2', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_007066.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004119.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related tyrosine kinase 3 (FLT3), transcript variant 1, mRNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'A more recent version of the selected reference sequence NM_004119.2 is available (NM_004119.3): NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT MUST be fully validated prior to use in reports: select_variants=NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}, 'NG_007066.1': {'end_exon': '14', 'start_exon': '14'}}}, 'NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': 'CCDS31953.1', 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': 'MANE'}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': True, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': True, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_457p1:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'lrg_tlr': 'LRG_457p1:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)', 'slr': 'NP_004110.2:p.(E608_N609delinsAGYEYDLKWEFPREI)', 'tlr': 'NP_004110.2:p.(Glu608_Asn609delinsAlaGlyTyrGluTyrAspLeuLysTrpGluPheProArgGluIle)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_004119.3:c.1821_1826delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos':

'28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_004110.2', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_004119.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related receptor tyrosine kinase 3 (FLT3), transcript variant 1, mRNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'NM_007166.3:c.1394A>G': {'alt_genomic_loci': [], 'annotations': {'chromosome': '11', 'db_xref': {'CCDS': 'CCDS8272.1', 'ensemblgene': None, 'hgnc': 'HGNC:15514', 'ncbigene': '8301', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '11q14.2', 'note': 'phosphatidylinositol binding clathrin assembly protein', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS55783', 'CCDS55784', 'CCDS8272', 'CCDS31653'], 'ensembl_gene_id': 'ENSG00000073921', 'entrez_gene_id': '8301', 'hgnc_id': 'HGNC:15514', 'omim_id': ['603025'], 'ucsc_id': 'uc001pbm.4'}, 'gene_symbol': 'PICALM', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_009097.2:p.(H465R)', 'tlr': 'NP_009097.2:p.(His465Arg)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_007166.3:c.1394A>G', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000011.9:g.85701307T>C', 'vcf': {'alt': 'C', 'chr': '11', 'pos': '85701307', 'ref': 'T'}}, 'grch38': {'hgvs_genomic_description': 'NC_000011.10:g.85990264T>C', 'vcf': {'alt': 'C', 'chr': '11', 'pos': '85990264', 'ref': 'T'}}, 'hg19': {'hgvs_genomic_description': 'NC_000011.9:g.85701307T>C', 'vcf': {'alt': 'C', 'chr': 'chr11', 'pos': '85701307', 'ref': 'T'}}, 'hg38': {'hgvs_genomic_description': 'NC_000011.10:g.85990264T>C', 'vcf': {'alt': 'C', 'chr': 'chr11', 'pos': '85990264', 'ref': 'T'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_009097.2', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_007166.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_007166.3:c.1394A>G', 'transcript_description': 'Homo sapiens phosphatidylinositol binding clathrin assembly protein (PICALM), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_007166.3 is available (NM_007166.4): NM_007166.4:c.1394A>G MUST be fully validated prior to use in reports: select_variants=NM_007166.4:c.1394A>G'], 'variant_exonic_positions': {'NC_000011.10': {'end_exon': '13', 'start_exon': '13'}, 'NC_000011.9': {'end_exon': '13', 'start_exon': '13'}}}, 'NM_016569.3:c.112C>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '12', 'db_xref': {'CCDS': 'CCDS9176.1', 'ensemblgene': None, 'hgnc': 'HGNC:11602', 'ncbigene': '6926', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '12q24.21', 'note': 'T-box transcription factor 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS9176', 'CCDS9175'], 'ensembl_gene_id': 'ENSG00000135111', 'entrez_gene_id': '6926', 'hgnc_id': 'HGNC:11602', 'omim_id': ['601621'], 'ucsc_id': 'uc001tvt.2'}, 'gene_symbol': 'TBX3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_057653.3:p.(P38T)', 'tlr': 'NP_057653.3:p.(Pro38Thr)'}, 'hgvs_refseqgene_variant': 'NG_008315.1:g.6076C>A', 'hgvs_transcript_variant': 'NM_016569.3:c.112C>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000012.11:g.115120894G>T', 'vcf': {'alt': 'T', 'chr': '12', 'pos': '115120894', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000012.12:g.114683089G>T', 'vcf': {'alt': 'T', 'chr': '12', 'pos': '114683089', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000012.11:g.115120894G>T', 'vcf': {'alt': 'T', 'chr': 'chr12', 'pos': '115120894', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000012.12:g.114683089G>T', 'vcf': {'alt': 'T', 'chr': 'chr12', 'pos': '114683089', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_057653.3', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_008315.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_016569.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_016569.3:c.112C>A', 'transcript_description': 'Homo sapiens T-box 3 (TBX3), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_016569.3 is available (NM_016569.4): NM_016569.4:c.112C>A MUST be fully validated prior to use in reports: select_variants=NM_016569.4:c.112C>A'], 'variant_exonic_positions': {'NC_000012.11': {'end_exon': '1', 'start_exon': '1'}, 'NC_000012.12': {'end_exon': '1', 'start_exon': '1'}, 'NG_008315.1': {'end_exon': '1', 'start_exon': '1'}}}, 'NM_020311.2:c.410G>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '2', 'db_xref': {'CCDS': 'CCDS2516.1', 'ensemblgene': None, 'hgnc': 'HGNC:23692', 'ncbigene': '57007', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '2q37.3', 'note': 'atypical chemokine receptor 3', 'refseq_select': False, 'variant': '0'}, 'gene_ids': {'ccds_ids': ['CCDS2516'], 'ensembl_gene_id': 'ENSG00000144476', 'entrez_gene_id': '57007', 'hgnc_id': 'HGNC:23692', 'omim_id': ['610376'], 'ucsc_id': ''}, 'gene_symbol': 'ACKR3', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_064707.1:p.(C137Y)', 'tlr': 'NP_064707.1:p.(Cys137Tyr)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_020311.2:c.410G>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000002.11:g.237489518G>A', 'vcf': {'alt': 'A', 'chr': '2', 'pos': '237489518', 'ref': 'G'}}, 'grch38': {'hgvs_genomic_description': 'NC_000002.12:g.236580875G>A', 'vcf': {'alt': 'A', 'chr': '2', 'pos': '236580875', 'ref': 'G'}}, 'hg19': {'hgvs_genomic_description': 'NC_000002.11:g.237489518G>A', 'vcf': {'alt': 'A', 'chr': 'chr2', 'pos': '237489518', 'ref': 'G'}}, 'hg38': {'hgvs_genomic_description': 'NC_000002.12:g.236580875G>A', 'vcf': {'alt': 'A', 'chr': 'chr2', 'pos': '236580875', 'ref': 'G'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_064707.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_020311.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_020311.2:c.410G>A', 'transcript_description': 'Homo sapiens atypical chemokine receptor 3 (ACKR3), mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_020311.2 is available (NM_020311.3): NM_020311.3:c.410G>A MUST be fully validated prior to use in reports: select_variants=NM_020311.3:c.410G>A'], 'variant_exonic_positions': {'NC_000002.11': {'end_exon': '2', 'start_exon': '2'}, 'NC_000002.12': {'end_exon': '2', 'start_exon': '2'}}}, 'NM_020975.4:c.166C>A': {'alt_genomic_loci': [], 'annotations': {'chromosome': '10', 'db_xref': {'CCDS': 'CCDS7200.1', 'ensemblgene': None, 'hgnc': 'HGNC:9967', 'ncbigene': '5979', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '10q11.21', 'note': 'ret proto-oncogene', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS7200', 'CCDS53525'], 'ensembl_gene_id': 'ENSG00000165731', 'entrez_gene_id': '5979', 'hgnc_id': 'HGNC:9967', 'omim_id': ['164761'], 'ucsc_id': 'uc001jal.4'}, 'gene_symbol': 'RET', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': 'LRG_518t1:c.166C>A', 'hgvs_lrg_variant': 'LRG_518:g.28483C>A', 'hgvs_predicted_protein_consequence': {'lrg_slr': 'LRG_518p1:p.(L56M)', 'lrg_tlr': 'LRG_518p1:p.(Leu56Met)', 'slr': 'NP_066124.1:p.(L56M)', 'tlr': 'NP_066124.1:p.(Leu56Met)'}, 'hgvs_refseqgene_variant': 'NG_007489.1:g.28483C>A', 'hgvs_transcript_variant': 'NM_020975.4:c.166C>A', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000010.10:g.43595999C>A', 'vcf': {'alt': 'A', 'chr': '10', 'pos': '43595999', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000010.11:g.43100551C>A', 'vcf': {'alt': 'A', 'chr': '10', 'pos': '43100551', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000010.10:g.43595999C>A',

'vcf': {'alt': 'A', 'chr': 'chr10', 'pos': '43595999', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000010.11:g.43100551C>A', 'vcf': {'alt': 'A', 'chr': 'chr10', 'pos': '43100551', 'ref': 'C'}}}, 'reference_sequence_records': {'lrg': 'http://ftp.ebi.ac.uk/pub/databases/lrgex/LRG_518.xml', 'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_066124.1', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_007489.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_020975.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_020975.4:c.166C>A', 'transcript_description': 'Homo sapiens ret proto-oncogene (RET), transcript variant 2, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_020975.4 is available (NM_020975.6): NM_020975.6:c.166C>A MUST be fully validated prior to use in reports: select_variants=NM_020975.6:c.166C>A'], 'variant_exonic_positions': {'NC_000010.10': {'end_exon': '2', 'start_exon': '2'}, 'NC_000010.11': {'end_exon': '2', 'start_exon': '2'}, 'NG_007489.1': {'end_exon': '2', 'start_exon': '2'}}}, 'NM_022768.4:c.623C>G': {'alt_genomic_loci': [], 'annotations': {'chromosome': '1', 'db_xref': {'CCDS': 'CCDS822.1', 'ensemblgene': None, 'hgnc': 'HGNC:14959', 'ncbigene': '64783', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '1p13.3', 'note': 'RNA binding motif protein 15', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS59198', 'CCDS822'], 'ensembl_gene_id': 'ENSG00000162775', 'entrez_gene_id': '64783', 'hgnc_id': 'HGNC:14959', 'omim_id': ['606077'], 'ucsc_id': 'uc021orn.2'}, 'gene_symbol': 'RBM15', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_073605.4:p.(S208W)', 'tlr': 'NP_073605.4:p.(Ser208Trp)'}, 'hgvs_refseqgene_variant': '', 'hgvs_transcript_variant': 'NM_022768.4:c.623C>G', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000001.10:g.110882650C>G', 'vcf': {'alt': 'G', 'chr': '1', 'pos': '110882650', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000001.11:g.110340028C>G', 'vcf': {'alt': 'G', 'chr': '1', 'pos': '110340028', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000001.10:g.110882650C>G', 'vcf': {'alt': 'G', 'chr': 'chr1', 'pos': '110882650', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000001.11:g.110340028C>G', 'vcf': {'alt': 'G', 'chr': 'chr1', 'pos': '110340028', 'ref': 'C'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_073605.4', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_022768.4'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_022768.4:c.623C>G', 'transcript_description': 'Homo sapiens RNA binding motif protein 15 (RBM15), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_022768.4 is available (NM_022768.5): NM_022768.5:c.623C>G MUST be fully validated prior to use in reports: select_variants=NM_022768.5:c.623C>G'], 'variant_exonic_positions': {'NC_000001.10': {'end_exon': '1', 'start_exon': '1'}, 'NC_000001.11': {'end_exon': '1', 'start_exon': '1'}}}, 'NM_133170.3:c.3982G>T': {'alt_genomic_loci': [], 'annotations': {'chromosome': '20', 'db_xref': {'CCDS': 'CCDS68127.1', 'ensemblgene': None, 'hgnc': 'HGNC:9682', 'ncbigene': '11122', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '20q12-q13.11', 'note': 'protein tyrosine phosphatase receptor type T', 'refseq_select': False, 'variant': '1'}, 'gene_ids': {'ccds_ids': ['CCDS42874', 'CCDS68127'], 'ensembl_gene_id': 'ENSG00000196090', 'entrez_gene_id': '11122', 'hgnc_id': 'HGNC:9682', 'omim_id': ['608712'], 'ucsc_id': 'uc061xcb.1'}, 'gene_symbol': 'PTPRT', 'genome_context_intronic_sequence': '', 'hgvs_lrg_transcript_variant': '', 'hgvs_lrg_variant': '', 'hgvs_predicted_protein_consequence': {'lrg_slr': '', 'lrg_tlr': '', 'slr': 'NP_573400.3:p.(D1328Y)', 'tlr': 'NP_573400.3:p.(Asp1328Tyr)'}, 'hgvs_refseqgene_variant': 'NG_033880.1:g.1109143G>T', 'hgvs_transcript_variant': 'NM_133170.3:c.3982G>T', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000020.10:g.40714415C>A', 'vcf': {'alt': 'A', 'chr': '20', 'pos': '40714415', 'ref': 'C'}}, 'grch38': {'hgvs_genomic_description': 'NC_000020.11:g.42085775C>A', 'vcf': {'alt': 'A', 'chr': '20', 'pos': '42085775', 'ref': 'C'}}, 'hg19': {'hgvs_genomic_description': 'NC_000020.10:g.40714415C>A', 'vcf': {'alt': 'A', 'chr': 'chr20', 'pos': '40714415', 'ref': 'C'}}, 'hg38': {'hgvs_genomic_description': 'NC_000020.11:g.42085775C>A', 'vcf': {'alt': 'A', 'chr': 'chr20', 'pos': '42085775', 'ref': 'C'}}}, 'reference_sequence_records': {'protein': 'https://www.ncbi.nlm.nih.gov/nuccore/NP_573400.3', 'refseqgene': 'https://www.ncbi.nlm.nih.gov/nuccore/NG_033880.1', 'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NM_133170.3'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'hg19', 'submitted_variant': 'NM_133170.3:c.3982G>T', 'transcript_description': 'Homo sapiens protein tyrosine phosphatase receptor type T (PTPRT), transcript variant 1, mRNA', 'validation_warnings': ['A more recent version of the selected reference sequence NM_133170.3 is available (NM_133170.4): NM_133170.4:c.3982G>T MUST be fully validated prior to use in reports: select_variants=NM_133170.4:c.3982G>T'], 'variant_exonic_positions': {'NC_000020.10': {'end_exon': '29', 'start_exon': '29'}, 'NC_000020.11': {'end_exon': '29', 'start_exon': '29'}, 'NG_033880.1': {'end_exon': '29', 'start_exon': '29'}}}, 'NR_130706.1:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': None, 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', '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': 'NR_130706.1:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci': {'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NR_130706.1'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related tyrosine kinase 3 (FLT3), transcript variant 2, non-coding RNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'A more recent version of the selected reference sequence NR_130706.1 is available (NR_130706.2): NR_130706.2:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT MUST be fully validated prior to use in reports: select_variants=NR_130706.2:n.1903_1908delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'NR_130706.2:n.1887_1892delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT': {'alt_genomic_loci': [], 'annotations': {'chromosome': '13', 'db_xref': {'CCDS': None, 'ensemblgene': None, 'hgnc': 'HGNC:3765', 'ncbigene': '2322', 'select': False}, 'ensembl_select': False, 'mane_plus_clinical': False, 'mane_select': False, 'map': '13q12.2', 'note': 'fms related receptor tyrosine kinase 3', 'refseq_select': False, 'variant': '2'}, 'gene_ids': {'ccds_ids': ['CCDS31953'], 'ensembl_gene_id': 'ENSG00000122025', 'entrez_gene_id': '2322', 'hgnc_id': 'HGNC:3765', 'omim_id': ['136351'], 'ucsc_id': 'uc001urw.3'}, 'gene_symbol': 'FLT3', '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': 'NR_130706.2:n.1887_1892delinsGGCCGGGTATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAT', 'primary_assembly_loci':

{'grch37': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'grch38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': '13', 'pos': '28034093', 'ref': 'TTTTCT'}}, 'hg19': {'hgvs_genomic_description': 'NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28608230', 'ref': 'TTTTCT'}}, 'hg38': {'hgvs_genomic_description': 'NC_000013.11:g.28034093_28034098delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'vcf': {'alt': 'ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'chr': 'chr13', 'pos': '28034093', 'ref': 'TTTTCT'}}}, 'reference_sequence_records': {'transcript': 'https://www.ncbi.nlm.nih.gov/nuccore/NR_130706.2'}, 'refseqgene_context_intronic_sequence': '', 'rna_variant_descriptions': None, 'selected_assembly': 'GRCh37', 'submitted_variant': '13:28608230:TTTTCT:ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC', 'transcript_description': 'Homo sapiens fms related receptor tyrosine kinase 3 (FLT3), transcript variant 2, non-coding RNA', 'validation_warnings': ['NC_000013.10:g.28608230TTTTCT>ATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC automapped to NC_000013.10:g.28608230_28608235delinsATTTCTCTTGGAAACTCCCATTTGAGATCATATTCATACCCGGCC'], 'variant_exonic_positions': {'NC_000013.10': {'end_exon': '14', 'start_exon': '14'}, 'NC_000013.11': {'end_exon': '14', 'start_exon': '14'}}}, 'flag': 'gene_variant', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

The second situation could explain the third one, the empty response:

{'flag': 'empty_result', 'metadata': {'variantvalidator_hgvs_version': '2.2.0', 'variantvalidator_version': '2.1.1.dev99+g5295451', 'vvdb_version': 'vvdb_2022_11', 'vvseqrepo_db': 'VV_SR_2022_11/master', 'vvta_version': 'vvta_2022_11_1'}}

For the moment, I have no cases of missing variants in a partially good response, but it could just be luck. I hope this helps.

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