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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: 4-1805643-A-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1805643&ref=A&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 1805643,
      "ref": "A",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000440486.8",
      "consequences": [
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1619A>C",
          "hgvs_p": "p.Asn540Thr",
          "transcript": "NM_000142.5",
          "protein_id": "NP_000133.1",
          "transcript_support_level": null,
          "aa_start": 540,
          "aa_end": null,
          "aa_length": 806,
          "cds_start": 1619,
          "cds_end": null,
          "cds_length": 2421,
          "cdna_start": 1894,
          "cdna_end": null,
          "cdna_length": 4301,
          "mane_select": "ENST00000440486.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1619A>C",
          "hgvs_p": "p.Asn540Thr",
          "transcript": "ENST00000440486.8",
          "protein_id": "ENSP00000414914.2",
          "transcript_support_level": 5,
          "aa_start": 540,
          "aa_end": null,
          "aa_length": 806,
          "cds_start": 1619,
          "cds_end": null,
          "cds_length": 2421,
          "cdna_start": 1894,
          "cdna_end": null,
          "cdna_length": 4301,
          "mane_select": "NM_000142.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1622A>C",
          "hgvs_p": "p.Asn541Thr",
          "transcript": "ENST00000481110.7",
          "protein_id": "ENSP00000420533.2",
          "transcript_support_level": 1,
          "aa_start": 541,
          "aa_end": null,
          "aa_length": 792,
          "cds_start": 1622,
          "cds_end": null,
          "cds_length": 2379,
          "cdna_start": 1889,
          "cdna_end": null,
          "cdna_length": 4149,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 9,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1283A>C",
          "hgvs_p": "p.Asn428Thr",
          "transcript": "ENST00000352904.6",
          "protein_id": "ENSP00000231803.1",
          "transcript_support_level": 1,
          "aa_start": 428,
          "aa_end": null,
          "aa_length": 694,
          "cds_start": 1283,
          "cds_end": null,
          "cds_length": 2085,
          "cdna_start": 1322,
          "cdna_end": null,
          "cdna_length": 2184,
          "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": 13,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "n.*675A>C",
          "hgvs_p": null,
          "transcript": "ENST00000260795.8",
          "protein_id": "ENSP00000260795.3",
          "transcript_support_level": 1,
          "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": 2841,
          "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": 13,
          "exon_rank_end": null,
          "exon_count": 19,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "n.*675A>C",
          "hgvs_p": null,
          "transcript": "ENST00000260795.8",
          "protein_id": "ENSP00000260795.3",
          "transcript_support_level": 1,
          "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": 2841,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1625A>C",
          "hgvs_p": "p.Asn542Thr",
          "transcript": "NM_001163213.2",
          "protein_id": "NP_001156685.1",
          "transcript_support_level": null,
          "aa_start": 542,
          "aa_end": null,
          "aa_length": 808,
          "cds_start": 1625,
          "cds_end": null,
          "cds_length": 2427,
          "cdna_start": 1900,
          "cdna_end": null,
          "cdna_length": 4307,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1625A>C",
          "hgvs_p": "p.Asn542Thr",
          "transcript": "ENST00000340107.9",
          "protein_id": "ENSP00000339824.4",
          "transcript_support_level": 5,
          "aa_start": 542,
          "aa_end": null,
          "aa_length": 808,
          "cds_start": 1625,
          "cds_end": null,
          "cds_length": 2427,
          "cdna_start": 1900,
          "cdna_end": null,
          "cdna_length": 4307,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1622A>C",
          "hgvs_p": "p.Asn541Thr",
          "transcript": "NM_001354809.2",
          "protein_id": "NP_001341738.1",
          "transcript_support_level": null,
          "aa_start": 541,
          "aa_end": null,
          "aa_length": 807,
          "cds_start": 1622,
          "cds_end": null,
          "cds_length": 2424,
          "cdna_start": 1897,
          "cdna_end": null,
          "cdna_length": 4304,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1607A>C",
          "hgvs_p": "p.Asn536Thr",
          "transcript": "ENST00000412135.7",
          "protein_id": "ENSP00000412903.3",
          "transcript_support_level": 5,
          "aa_start": 536,
          "aa_end": null,
          "aa_length": 802,
          "cds_start": 1607,
          "cds_end": null,
          "cds_length": 2409,
          "cdna_start": 1882,
          "cdna_end": null,
          "cdna_length": 4294,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1622A>C",
          "hgvs_p": "p.Asn541Thr",
          "transcript": "NM_001354810.2",
          "protein_id": "NP_001341739.1",
          "transcript_support_level": null,
          "aa_start": 541,
          "aa_end": null,
          "aa_length": 792,
          "cds_start": 1622,
          "cds_end": null,
          "cds_length": 2379,
          "cdna_start": 1897,
          "cdna_end": null,
          "cdna_length": 4233,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1283A>C",
          "hgvs_p": "p.Asn428Thr",
          "transcript": "NM_022965.4",
          "protein_id": "NP_075254.1",
          "transcript_support_level": null,
          "aa_start": 428,
          "aa_end": null,
          "aa_length": 694,
          "cds_start": 1283,
          "cds_end": null,
          "cds_length": 2085,
          "cdna_start": 1558,
          "cdna_end": null,
          "cdna_length": 3965,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1631A>C",
          "hgvs_p": "p.Asn544Thr",
          "transcript": "XM_006713868.2",
          "protein_id": "XP_006713931.1",
          "transcript_support_level": null,
          "aa_start": 544,
          "aa_end": null,
          "aa_length": 811,
          "cds_start": 1631,
          "cds_end": null,
          "cds_length": 2436,
          "cdna_start": 1906,
          "cdna_end": null,
          "cdna_length": 4316,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1631A>C",
          "hgvs_p": "p.Asn544Thr",
          "transcript": "XM_047449820.1",
          "protein_id": "XP_047305776.1",
          "transcript_support_level": null,
          "aa_start": 544,
          "aa_end": null,
          "aa_length": 811,
          "cds_start": 1631,
          "cds_end": null,
          "cds_length": 2436,
          "cdna_start": 1783,
          "cdna_end": null,
          "cdna_length": 4193,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1631A>C",
          "hgvs_p": "p.Asn544Thr",
          "transcript": "XM_006713869.2",
          "protein_id": "XP_006713932.1",
          "transcript_support_level": null,
          "aa_start": 544,
          "aa_end": null,
          "aa_length": 810,
          "cds_start": 1631,
          "cds_end": null,
          "cds_length": 2433,
          "cdna_start": 1906,
          "cdna_end": null,
          "cdna_length": 4313,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1628A>C",
          "hgvs_p": "p.Asn543Thr",
          "transcript": "XM_006713870.2",
          "protein_id": "XP_006713933.1",
          "transcript_support_level": null,
          "aa_start": 543,
          "aa_end": null,
          "aa_length": 810,
          "cds_start": 1628,
          "cds_end": null,
          "cds_length": 2433,
          "cdna_start": 1903,
          "cdna_end": null,
          "cdna_length": 4313,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1625A>C",
          "hgvs_p": "p.Asn542Thr",
          "transcript": "XM_006713871.2",
          "protein_id": "XP_006713934.1",
          "transcript_support_level": null,
          "aa_start": 542,
          "aa_end": null,
          "aa_length": 809,
          "cds_start": 1625,
          "cds_end": null,
          "cds_length": 2430,
          "cdna_start": 1900,
          "cdna_end": null,
          "cdna_length": 4310,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1625A>C",
          "hgvs_p": "p.Asn542Thr",
          "transcript": "XM_011513420.2",
          "protein_id": "XP_011511722.1",
          "transcript_support_level": null,
          "aa_start": 542,
          "aa_end": null,
          "aa_length": 809,
          "cds_start": 1625,
          "cds_end": null,
          "cds_length": 2430,
          "cdna_start": 1900,
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          "cdna_length": 4310,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1628A>C",
          "hgvs_p": "p.Asn543Thr",
          "transcript": "XM_047449821.1",
          "protein_id": "XP_047305777.1",
          "transcript_support_level": null,
          "aa_start": 543,
          "aa_end": null,
          "aa_length": 809,
          "cds_start": 1628,
          "cds_end": null,
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          "cdna_start": 1903,
          "cdna_end": null,
          "cdna_length": 4310,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "c.1622A>C",
          "hgvs_p": "p.Asn541Thr",
          "transcript": "XM_011513422.2",
          "protein_id": "XP_011511724.1",
          "transcript_support_level": null,
          "aa_start": 541,
          "aa_end": null,
          "aa_length": 808,
          "cds_start": 1622,
          "cds_end": null,
          "cds_length": 2427,
          "cdna_start": 1897,
          "cdna_end": null,
          "cdna_length": 4307,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
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          "gene_symbol": "FGFR3",
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          "exon_count": 17,
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          "transcript": "XM_047449822.1",
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        },
        {
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          "transcript": "XM_047449823.1",
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        {
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          "strand": true,
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          ],
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          "exon_count": 17,
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          "gene_symbol": "FGFR3",
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          "hgvs_c": "c.1619A>C",
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          "transcript": "XM_047449824.1",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
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          "exon_rank": 3,
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          "exon_count": 4,
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          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "n.685A>C",
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          "transcript": "ENST00000469068.1",
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          "transcript_support_level": 3,
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          "aa_length": null,
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        },
        {
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          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 13,
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          "exon_count": 19,
          "intron_rank": null,
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          "gene_symbol": "FGFR3",
          "gene_hgnc_id": 3690,
          "hgvs_c": "n.2045A>C",
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          "transcript": "NR_148971.2",
          "protein_id": null,
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          "aa_length": null,
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          "cdna_length": 4452,
          "mane_select": null,
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        }
      ],
      "gene_symbol": "FGFR3",
      "gene_hgnc_id": 3690,
      "dbsnp": "rs77722678",
      "frequency_reference_population": 6.845189e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.84519e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.9932390451431274,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.796,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.7461,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.06,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 8.73,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0.01,
      "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": 18,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 18,
          "benign_score": 0,
          "pathogenic_score": 18,
          "criteria": [
            "PM1",
            "PM2",
            "PM5",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000440486.8",
          "gene_symbol": "FGFR3",
          "hgnc_id": 3690,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR,SD",
          "hgvs_c": "c.1619A>C",
          "hgvs_p": "p.Asn540Thr"
        }
      ],
      "clinvar_disease": "Hypochondroplasia,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:1 LP:2",
      "phenotype_combined": "Hypochondroplasia|not provided",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}