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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 10-73500799-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=73500799&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "10",
      "pos": 73500799,
      "ref": "G",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_001391941.1",
      "consequences": [
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4351C>T",
          "hgvs_p": "p.Arg1451Cys",
          "transcript": "NM_001391956.1",
          "protein_id": "NP_001378885.1",
          "transcript_support_level": null,
          "aa_start": 1451,
          "aa_end": null,
          "aa_length": 1684,
          "cds_start": 4351,
          "cds_end": null,
          "cds_length": 5055,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000687698.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391956.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4351C>T",
          "hgvs_p": "p.Arg1451Cys",
          "transcript": "ENST00000687698.1",
          "protein_id": "ENSP00000510226.1",
          "transcript_support_level": null,
          "aa_start": 1451,
          "aa_end": null,
          "aa_length": 1684,
          "cds_start": 4351,
          "cds_end": null,
          "cds_length": 5055,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001391956.1",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000687698.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": 19,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.*1461-1611C>T",
          "hgvs_p": null,
          "transcript": "ENST00000422491.7",
          "protein_id": "ENSP00000407368.4",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 837,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 2514,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000422491.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "PPP3CB-AS1",
          "gene_hgnc_id": 50750,
          "hgvs_c": "n.1298+1112G>A",
          "hgvs_p": null,
          "transcript": "ENST00000422977.3",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000422977.3"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4417C>T",
          "hgvs_p": "p.Arg1473Cys",
          "transcript": "NM_001391941.1",
          "protein_id": "NP_001378870.1",
          "transcript_support_level": null,
          "aa_start": 1473,
          "aa_end": null,
          "aa_length": 1706,
          "cds_start": 4417,
          "cds_end": null,
          "cds_length": 5121,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391941.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4351C>T",
          "hgvs_p": "p.Arg1451Cys",
          "transcript": "NM_001391953.1",
          "protein_id": "NP_001378882.1",
          "transcript_support_level": null,
          "aa_start": 1451,
          "aa_end": null,
          "aa_length": 1684,
          "cds_start": 4351,
          "cds_end": null,
          "cds_length": 5055,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391953.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4351C>T",
          "hgvs_p": "p.Arg1451Cys",
          "transcript": "NM_152586.4",
          "protein_id": "NP_689799.3",
          "transcript_support_level": null,
          "aa_start": 1451,
          "aa_end": null,
          "aa_length": 1684,
          "cds_start": 4351,
          "cds_end": null,
          "cds_length": 5055,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_152586.4"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4351C>T",
          "hgvs_p": "p.Arg1451Cys",
          "transcript": "ENST00000339859.8",
          "protein_id": "ENSP00000345216.4",
          "transcript_support_level": 5,
          "aa_start": 1451,
          "aa_end": null,
          "aa_length": 1684,
          "cds_start": 4351,
          "cds_end": null,
          "cds_length": 5055,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000339859.8"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4246C>T",
          "hgvs_p": "p.Arg1416Cys",
          "transcript": "ENST00000928943.1",
          "protein_id": "ENSP00000599002.1",
          "transcript_support_level": null,
          "aa_start": 1416,
          "aa_end": null,
          "aa_length": 1649,
          "cds_start": 4246,
          "cds_end": null,
          "cds_length": 4950,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000928943.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4246C>T",
          "hgvs_p": "p.Arg1416Cys",
          "transcript": "ENST00000928945.1",
          "protein_id": "ENSP00000599004.1",
          "transcript_support_level": null,
          "aa_start": 1416,
          "aa_end": null,
          "aa_length": 1649,
          "cds_start": 4246,
          "cds_end": null,
          "cds_length": 4950,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000928945.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4231C>T",
          "hgvs_p": "p.Arg1411Cys",
          "transcript": "ENST00000689425.1",
          "protein_id": "ENSP00000508413.1",
          "transcript_support_level": null,
          "aa_start": 1411,
          "aa_end": null,
          "aa_length": 1644,
          "cds_start": 4231,
          "cds_end": null,
          "cds_length": 4935,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000689425.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4210C>T",
          "hgvs_p": "p.Arg1404Cys",
          "transcript": "NM_001391949.1",
          "protein_id": "NP_001378878.1",
          "transcript_support_level": null,
          "aa_start": 1404,
          "aa_end": null,
          "aa_length": 1637,
          "cds_start": 4210,
          "cds_end": null,
          "cds_length": 4914,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391949.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4210C>T",
          "hgvs_p": "p.Arg1404Cys",
          "transcript": "NM_001391952.1",
          "protein_id": "NP_001378881.1",
          "transcript_support_level": null,
          "aa_start": 1404,
          "aa_end": null,
          "aa_length": 1637,
          "cds_start": 4210,
          "cds_end": null,
          "cds_length": 4914,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391952.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4210C>T",
          "hgvs_p": "p.Arg1404Cys",
          "transcript": "ENST00000681793.1",
          "protein_id": "ENSP00000505692.1",
          "transcript_support_level": null,
          "aa_start": 1404,
          "aa_end": null,
          "aa_length": 1637,
          "cds_start": 4210,
          "cds_end": null,
          "cds_length": 4914,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000681793.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001378208.1",
          "protein_id": "NP_001365137.1",
          "transcript_support_level": null,
          "aa_start": 1394,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001378208.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001378209.1",
          "protein_id": "NP_001365138.1",
          "transcript_support_level": null,
          "aa_start": 1394,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001378209.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001378210.1",
          "protein_id": "NP_001365139.1",
          "transcript_support_level": null,
          "aa_start": 1394,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "NM_001378210.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001391945.1",
          "protein_id": "NP_001378874.1",
          "transcript_support_level": null,
          "aa_start": 1394,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391945.1"
        },
        {
          "aa_ref": "R",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001391946.1",
          "protein_id": "NP_001378875.1",
          "transcript_support_level": null,
          "aa_start": 1394,
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          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001391946.1"
        },
        {
          "aa_ref": "R",
          "aa_alt": "C",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 21,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "USP54",
          "gene_hgnc_id": 23513,
          "hgvs_c": "c.4180C>T",
          "hgvs_p": "p.Arg1394Cys",
          "transcript": "NM_001391948.1",
          "protein_id": "NP_001378877.1",
          "transcript_support_level": null,
          "aa_start": 1394,
          "aa_end": null,
          "aa_length": 1627,
          "cds_start": 4180,
          "cds_end": null,
          "cds_length": 4884,
          "cdna_start": null,
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        {
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          "biotype": "pseudogene",
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      ],
      "gene_symbol": "USP54",
      "gene_hgnc_id": 23513,
      "dbsnp": "rs138141992",
      "frequency_reference_population": 0.00024700345,
      "hom_count_reference_population": 1,
      "allele_count_reference_population": 395,
      "gnomad_exomes_af": 0.000129928,
      "gnomad_genomes_af": 0.00135989,
      "gnomad_exomes_ac": 188,
      "gnomad_genomes_ac": 207,
      "gnomad_exomes_homalt": 1,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.007691860198974609,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.05999999865889549,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.125,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.1027,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.28,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 5.623,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.06,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -4,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong",
      "acmg_by_gene": [
        {
          "score": -4,
          "benign_score": 4,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001391941.1",
          "gene_symbol": "USP54",
          "hgnc_id": 23513,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.4417C>T",
          "hgvs_p": "p.Arg1473Cys"
        },
        {
          "score": -4,
          "benign_score": 4,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000422977.3",
          "gene_symbol": "PPP3CB-AS1",
          "hgnc_id": 50750,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.1298+1112G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "USP54-related disorder",
      "clinvar_classification": "Likely benign",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "USP54-related disorder",
      "pathogenicity_classification_combined": "Likely benign",
      "custom_annotations": null
    }
  ],
  "message": null
}