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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: 9-35792502-C-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=35792502&ref=C&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "9",
      "pos": 35792502,
      "ref": "C",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_003995.4",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "NM_003995.4",
          "protein_id": "NP_003986.2",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1047,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3144,
          "cdna_start": 912,
          "cdna_end": null,
          "cdna_length": 4248,
          "mane_select": "ENST00000342694.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000342694.7",
          "protein_id": "ENSP00000341083.2",
          "transcript_support_level": 1,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1047,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3144,
          "cdna_start": 912,
          "cdna_end": null,
          "cdna_length": 4248,
          "mane_select": "NM_003995.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000687787.1",
          "protein_id": "ENSP00000509440.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1100,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3303,
          "cdna_start": 94,
          "cdna_end": null,
          "cdna_length": 3561,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000693094.1",
          "protein_id": "ENSP00000510161.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1077,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3234,
          "cdna_start": 94,
          "cdna_end": null,
          "cdna_length": 3485,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000690070.1",
          "protein_id": "ENSP00000509654.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1075,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3228,
          "cdna_start": 94,
          "cdna_end": null,
          "cdna_length": 3486,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "NM_001378923.1",
          "protein_id": "NP_001365852.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1050,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3153,
          "cdna_start": 912,
          "cdna_end": null,
          "cdna_length": 4257,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000685871.1",
          "protein_id": "ENSP00000509964.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": 174,
          "cdna_end": null,
          "cdna_length": 3410,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr",
          "transcript": "ENST00000687357.1",
          "protein_id": "ENSP00000509549.1",
          "transcript_support_level": null,
          "aa_start": 32,
          "aa_end": null,
          "aa_length": 998,
          "cds_start": 94,
          "cds_end": null,
          "cds_length": 2997,
          "cdna_start": 94,
          "cdna_end": null,
          "cdna_length": 3255,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
          "hgvs_p": null,
          "transcript": "ENST00000448821.6",
          "protein_id": "ENSP00000402902.2",
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3243,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
          "hgvs_p": null,
          "transcript": "ENST00000464810.5",
          "protein_id": null,
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 3502,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.133C>A",
          "hgvs_p": null,
          "transcript": "ENST00000686159.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
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          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 3456,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 2,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.126C>A",
          "hgvs_p": null,
          "transcript": "ENST00000688201.1",
          "protein_id": null,
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          "mane_select": null,
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        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.175C>A",
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          "transcript": "ENST00000688869.1",
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        {
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
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          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
          "hgvs_p": null,
          "transcript": "ENST00000689788.1",
          "protein_id": "ENSP00000508973.1",
          "transcript_support_level": null,
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          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "consequences": [
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          ],
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          "exon_count": 20,
          "intron_rank": null,
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          "gene_symbol": "NPR2",
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        {
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          ],
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          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
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          "transcript": "ENST00000690267.1",
          "protein_id": "ENSP00000510432.1",
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          "mane_select": null,
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        },
        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
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          "transcript": "ENST00000691969.1",
          "protein_id": "ENSP00000510244.1",
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
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          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
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        {
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          ],
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          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": null,
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          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.94C>A",
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        },
        {
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          "canonical": false,
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          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "intron_rank": 1,
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          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.164+1336C>A",
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          "transcript": "ENST00000687625.1",
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          "cdna_length": 2557,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 20,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.164+1336C>A",
          "hgvs_p": null,
          "transcript": "ENST00000692380.1",
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          "transcript": "ENST00000687302.1",
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        },
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          ],
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          "exon_count": 21,
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          "gene_symbol": "NPR2",
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          "hgvs_c": "n.-46C>A",
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          "transcript": "ENST00000690552.1",
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          "aa_length": null,
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          "cdna_start": null,
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          "cdna_length": 3740,
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 19,
          "intron_rank": null,
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          "gene_symbol": "NPR2",
          "gene_hgnc_id": 7944,
          "hgvs_c": "n.-46C>A",
          "hgvs_p": null,
          "transcript": "ENST00000691138.1",
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          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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        },
        {
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          "consequences": [
            "upstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 2,
          "intron_rank": null,
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          "gene_symbol": "ENSG00000297929",
          "gene_hgnc_id": null,
          "hgvs_c": "n.-77G>T",
          "hgvs_p": null,
          "transcript": "ENST00000751870.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_length": 830,
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        }
      ],
      "gene_symbol": "NPR2",
      "gene_hgnc_id": 7944,
      "dbsnp": "rs28931581",
      "frequency_reference_population": null,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 0,
      "gnomad_exomes_af": null,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": null,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": null,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9764993190765381,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.689,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9827,
      "alphamissense_prediction": "Pathogenic",
      "bayesdelnoaf_score": 0.29,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.401,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0,
      "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": 7,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PM2,PP2,PP3_Strong",
      "acmg_by_gene": [
        {
          "score": 7,
          "benign_score": 0,
          "pathogenic_score": 7,
          "criteria": [
            "PM2",
            "PP2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NM_003995.4",
          "gene_symbol": "NPR2",
          "hgnc_id": 7944,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.94C>A",
          "hgvs_p": "p.Pro32Thr"
        },
        {
          "score": 6,
          "benign_score": 0,
          "pathogenic_score": 6,
          "criteria": [
            "PM2",
            "PP3_Strong"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000751870.1",
          "gene_symbol": "ENSG00000297929",
          "hgnc_id": null,
          "effects": [
            "upstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.-77G>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " Maroteaux type,Acromesomelic dysplasia 1,Tall stature-scoliosis-macrodactyly of the great toes syndrome",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "Acromesomelic dysplasia 1, Maroteaux type|Tall stature-scoliosis-macrodactyly of the great toes syndrome;Acromesomelic dysplasia 1, Maroteaux type",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}