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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: 7-117611671-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=117611671&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "7",
      "pos": 117611671,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_000492.4",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3230T>C",
          "hgvs_p": "p.Leu1077Pro",
          "transcript": "NM_000492.4",
          "protein_id": "NP_000483.3",
          "transcript_support_level": null,
          "aa_start": 1077,
          "aa_end": null,
          "aa_length": 1480,
          "cds_start": 3230,
          "cds_end": null,
          "cds_length": 4443,
          "cdna_start": 3300,
          "cdna_end": null,
          "cdna_length": 6070,
          "mane_select": "ENST00000003084.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3230T>C",
          "hgvs_p": "p.Leu1077Pro",
          "transcript": "ENST00000003084.11",
          "protein_id": "ENSP00000003084.6",
          "transcript_support_level": 1,
          "aa_start": 1077,
          "aa_end": null,
          "aa_length": 1480,
          "cds_start": 3230,
          "cds_end": null,
          "cds_length": 4443,
          "cdna_start": 3300,
          "cdna_end": null,
          "cdna_length": 6070,
          "mane_select": "NM_000492.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3230T>C",
          "hgvs_p": "p.Leu1077Pro",
          "transcript": "ENST00000699602.1",
          "protein_id": "ENSP00000514471.1",
          "transcript_support_level": null,
          "aa_start": 1077,
          "aa_end": null,
          "aa_length": 1478,
          "cds_start": 3230,
          "cds_end": null,
          "cds_length": 4437,
          "cdna_start": 3337,
          "cdna_end": null,
          "cdna_length": 6024,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3140T>C",
          "hgvs_p": "p.Leu1047Pro",
          "transcript": "ENST00000426809.5",
          "protein_id": "ENSP00000389119.1",
          "transcript_support_level": 5,
          "aa_start": 1047,
          "aa_end": null,
          "aa_length": 1437,
          "cds_start": 3140,
          "cds_end": null,
          "cds_length": 4316,
          "cdna_start": 3140,
          "cdna_end": null,
          "cdna_length": 4316,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3047T>C",
          "hgvs_p": "p.Leu1016Pro",
          "transcript": "ENST00000649781.2",
          "protein_id": "ENSP00000497203.1",
          "transcript_support_level": null,
          "aa_start": 1016,
          "aa_end": null,
          "aa_length": 1419,
          "cds_start": 3047,
          "cds_end": null,
          "cds_length": 4260,
          "cdna_start": 3131,
          "cdna_end": null,
          "cdna_length": 5824,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.2804T>C",
          "hgvs_p": "p.Leu935Pro",
          "transcript": "ENST00000699605.1",
          "protein_id": "ENSP00000514473.1",
          "transcript_support_level": null,
          "aa_start": 935,
          "aa_end": null,
          "aa_length": 1338,
          "cds_start": 2804,
          "cds_end": null,
          "cds_length": 4017,
          "cdna_start": 3226,
          "cdna_end": null,
          "cdna_length": 5919,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 19,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.3047T>C",
          "hgvs_p": "p.Leu1016Pro",
          "transcript": "ENST00000649406.1",
          "protein_id": "ENSP00000497965.1",
          "transcript_support_level": null,
          "aa_start": 1016,
          "aa_end": null,
          "aa_length": 1187,
          "cds_start": 3047,
          "cds_end": null,
          "cds_length": 3564,
          "cdna_start": 3131,
          "cdna_end": null,
          "cdna_length": 3758,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.2012T>C",
          "hgvs_p": "p.Leu671Pro",
          "transcript": "ENST00000648260.1",
          "protein_id": "ENSP00000497957.1",
          "transcript_support_level": null,
          "aa_start": 671,
          "aa_end": null,
          "aa_length": 842,
          "cds_start": 2012,
          "cds_end": null,
          "cds_length": 2529,
          "cdna_start": 2096,
          "cdna_end": null,
          "cdna_length": 2723,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "c.53T>C",
          "hgvs_p": "p.Leu18Pro",
          "transcript": "ENST00000468795.1",
          "protein_id": "ENSP00000419254.1",
          "transcript_support_level": 5,
          "aa_start": 18,
          "aa_end": null,
          "aa_length": 189,
          "cds_start": 53,
          "cds_end": null,
          "cds_length": 570,
          "cdna_start": 55,
          "cdna_end": null,
          "cdna_length": 682,
          "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": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000647720.2",
          "protein_id": "ENSP00000497673.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 5804,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.*2944T>C",
          "hgvs_p": null,
          "transcript": "ENST00000647978.2",
          "protein_id": "ENSP00000497658.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 5898,
          "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": 20,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000685018.2",
          "protein_id": "ENSP00000510194.2",
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          "cdna_start": null,
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          "cdna_length": 6223,
          "mane_select": null,
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        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000687278.2",
          "protein_id": "ENSP00000509593.2",
          "transcript_support_level": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699585.1",
          "protein_id": "ENSP00000514456.1",
          "transcript_support_level": null,
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          "cdna_length": 6065,
          "mane_select": null,
          "mane_plus": null,
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        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": true,
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            "non_coding_transcript_exon_variant"
          ],
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          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
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          "hgvs_c": "n.3230T>C",
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          "transcript": "ENST00000699598.1",
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        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699599.1",
          "protein_id": "ENSP00000514468.1",
          "transcript_support_level": null,
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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": 20,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.3230T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699600.1",
          "protein_id": "ENSP00000514469.1",
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          "cdna_length": 4793,
          "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": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.*1530T>C",
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          "transcript": "ENST00000699601.1",
          "protein_id": "ENSP00000514470.1",
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        {
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          "strand": true,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
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          "hgvs_c": "n.*3054T>C",
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          "transcript": "ENST00000699604.1",
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          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.*2944T>C",
          "hgvs_p": null,
          "transcript": "ENST00000647978.2",
          "protein_id": "ENSP00000497658.1",
          "transcript_support_level": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 5898,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.*1530T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699601.1",
          "protein_id": "ENSP00000514470.1",
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 6100,
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 20,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
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          "gene_symbol": "CFTR",
          "gene_hgnc_id": 1884,
          "hgvs_c": "n.*3054T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699604.1",
          "protein_id": "ENSP00000514472.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 6005,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000083622",
          "gene_hgnc_id": null,
          "hgvs_c": "n.177+4558A>G",
          "hgvs_p": null,
          "transcript": "ENST00000456270.1",
          "protein_id": null,
          "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": 376,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "CFTR-AS2",
          "gene_hgnc_id": 40145,
          "hgvs_c": "n.177+4558A>G",
          "hgvs_p": null,
          "transcript": "NR_199597.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": 376,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "CFTR",
      "gene_hgnc_id": 1884,
      "dbsnp": "rs139304906",
      "frequency_reference_population": 0.0000030988265,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 5,
      "gnomad_exomes_af": 0.00000273709,
      "gnomad_genomes_af": 0.00000657428,
      "gnomad_exomes_ac": 4,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8649692535400391,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.834,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9761,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.4,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.929,
      "phylop100way_prediction": "Pathogenic",
      "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": 15,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PP2,PP3_Moderate,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 15,
          "benign_score": 0,
          "pathogenic_score": 15,
          "criteria": [
            "PM1",
            "PM2",
            "PP2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_000492.4",
          "gene_symbol": "CFTR",
          "hgnc_id": 1884,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.3230T>C",
          "hgvs_p": "p.Leu1077Pro"
        },
        {
          "score": 12,
          "benign_score": 0,
          "pathogenic_score": 12,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000456270.1",
          "gene_symbol": "ENSG00000083622",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.177+4558A>G",
          "hgvs_p": null
        },
        {
          "score": 12,
          "benign_score": 0,
          "pathogenic_score": 12,
          "criteria": [
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NR_199597.1",
          "gene_symbol": "CFTR-AS2",
          "hgnc_id": 40145,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.177+4558A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Bronchiectasis with or without elevated sweat chloride 1,CFTR-related disorder,Congenital bilateral aplasia of vas deferens from CFTR mutation,Cystic fibrosis,Hereditary pancreatitis,not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "reviewed by expert panel",
      "clinvar_submissions_summary": "P:12 LP:1",
      "phenotype_combined": "Cystic fibrosis|Cystic fibrosis;Congenital bilateral aplasia of vas deferens from CFTR mutation|CFTR-related disorder|not provided|Cystic fibrosis;Congenital bilateral aplasia of vas deferens from CFTR mutation;Bronchiectasis with or without elevated sweat chloride 1;Hereditary pancreatitis|Bronchiectasis with or without elevated sweat chloride 1",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}