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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: 16-53622339-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=53622339&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 53622339,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "ENST00000647211.2",
      "consequences": [
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3312C>T",
          "hgvs_p": "p.Pro1104Pro",
          "transcript": "NM_015272.5",
          "protein_id": "NP_056087.2",
          "transcript_support_level": null,
          "aa_start": 1104,
          "aa_end": null,
          "aa_length": 1315,
          "cds_start": 3312,
          "cds_end": null,
          "cds_length": 3948,
          "cdna_start": 3376,
          "cdna_end": null,
          "cdna_length": 7935,
          "mane_select": "ENST00000647211.2",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3312C>T",
          "hgvs_p": "p.Pro1104Pro",
          "transcript": "ENST00000647211.2",
          "protein_id": "ENSP00000493946.1",
          "transcript_support_level": null,
          "aa_start": 1104,
          "aa_end": null,
          "aa_length": 1315,
          "cds_start": 3312,
          "cds_end": null,
          "cds_length": 3948,
          "cdna_start": 3376,
          "cdna_end": null,
          "cdna_length": 7935,
          "mane_select": "NM_015272.5",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3210C>T",
          "hgvs_p": "p.Pro1070Pro",
          "transcript": "ENST00000563746.5",
          "protein_id": "ENSP00000457889.1",
          "transcript_support_level": 1,
          "aa_start": 1070,
          "aa_end": null,
          "aa_length": 1281,
          "cds_start": 3210,
          "cds_end": null,
          "cds_length": 3846,
          "cdna_start": 3262,
          "cdna_end": null,
          "cdna_length": 4193,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "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": 26,
          "intron_rank": 22,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3295-3131C>T",
          "hgvs_p": null,
          "transcript": "ENST00000621565.5",
          "protein_id": "ENSP00000480698.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 1269,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3810,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 6678,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3210C>T",
          "hgvs_p": "p.Pro1070Pro",
          "transcript": "NM_001330538.2",
          "protein_id": "NP_001317467.1",
          "transcript_support_level": null,
          "aa_start": 1070,
          "aa_end": null,
          "aa_length": 1281,
          "cds_start": 3210,
          "cds_end": null,
          "cds_length": 3846,
          "cdna_start": 3274,
          "cdna_end": null,
          "cdna_length": 7833,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3324C>T",
          "hgvs_p": "p.Pro1108Pro",
          "transcript": "XM_047433869.1",
          "protein_id": "XP_047289825.1",
          "transcript_support_level": null,
          "aa_start": 1108,
          "aa_end": null,
          "aa_length": 1319,
          "cds_start": 3324,
          "cds_end": null,
          "cds_length": 3960,
          "cdna_start": 3636,
          "cdna_end": null,
          "cdna_length": 8195,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 27,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3312C>T",
          "hgvs_p": "p.Pro1104Pro",
          "transcript": "XM_047433870.1",
          "protein_id": "XP_047289826.1",
          "transcript_support_level": null,
          "aa_start": 1104,
          "aa_end": null,
          "aa_length": 1315,
          "cds_start": 3312,
          "cds_end": null,
          "cds_length": 3948,
          "cdna_start": 3624,
          "cdna_end": null,
          "cdna_length": 8183,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 22,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3210C>T",
          "hgvs_p": "p.Pro1070Pro",
          "transcript": "XM_047433871.1",
          "protein_id": "XP_047289827.1",
          "transcript_support_level": null,
          "aa_start": 1070,
          "aa_end": null,
          "aa_length": 1281,
          "cds_start": 3210,
          "cds_end": null,
          "cds_length": 3846,
          "cdna_start": 3522,
          "cdna_end": null,
          "cdna_length": 8081,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.1557C>T",
          "hgvs_p": "p.Pro519Pro",
          "transcript": "XM_017023098.2",
          "protein_id": "XP_016878587.1",
          "transcript_support_level": null,
          "aa_start": 519,
          "aa_end": null,
          "aa_length": 730,
          "cds_start": 1557,
          "cds_end": null,
          "cds_length": 2193,
          "cdna_start": 2317,
          "cdna_end": null,
          "cdna_length": 6876,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "P",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 10,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.1557C>T",
          "hgvs_p": "p.Pro519Pro",
          "transcript": "XM_017023099.2",
          "protein_id": "XP_016878588.1",
          "transcript_support_level": null,
          "aa_start": 519,
          "aa_end": null,
          "aa_length": 730,
          "cds_start": 1557,
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          "cdna_start": 1677,
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          "cdna_length": 6236,
          "mane_select": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.3736C>T",
          "hgvs_p": null,
          "transcript": "ENST00000565343.2",
          "protein_id": null,
          "transcript_support_level": 5,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
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          "mane_select": null,
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
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          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.*72C>T",
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          "transcript": "ENST00000680193.1",
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        {
          "aa_ref": null,
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          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.3274C>T",
          "hgvs_p": null,
          "transcript": "XR_007064860.1",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "3_prime_UTR_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.*72C>T",
          "hgvs_p": null,
          "transcript": "ENST00000680193.1",
          "protein_id": "ENSP00000506379.1",
          "transcript_support_level": null,
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        },
        {
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          ],
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          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3295-3131C>T",
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        },
        {
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          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 25,
          "intron_rank": 22,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3295-3131C>T",
          "hgvs_p": null,
          "transcript": "ENST00000564374.5",
          "protein_id": "ENSP00000456534.1",
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          "aa_start": null,
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          "aa_length": 1253,
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 25,
          "intron_rank": 21,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3193-3131C>T",
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          "transcript": "NM_001127897.4",
          "protein_id": "NP_001121369.1",
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          "cdna_start": null,
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        {
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          "canonical": false,
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          ],
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          "intron_rank": 21,
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          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3193-3131C>T",
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          "transcript": "ENST00000262135.9",
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        },
        {
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          "canonical": false,
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          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": 4,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.1205-3131C>T",
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 27,
          "intron_rank": 23,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "c.3307-3131C>T",
          "hgvs_p": null,
          "transcript": "XM_005255868.3",
          "protein_id": "XP_005255925.1",
          "transcript_support_level": null,
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          "aa_length": 1273,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 3822,
          "cdna_start": null,
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          "cdna_length": 7809,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "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": 26,
          "intron_rank": 22,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
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          "transcript": "XM_017023095.3",
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          "cds_length": 3720,
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          "exon_count": 25,
          "intron_rank": 21,
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          "hgvs_c": "c.3193-3131C>T",
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          "transcript": "XM_047433872.1",
          "protein_id": "XP_047289828.1",
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          "cds_start": -4,
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        },
        {
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          "protein_coding": false,
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            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 26,
          "intron_rank": 22,
          "intron_rank_end": null,
          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.3359-3131C>T",
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          "transcript": "XR_007064861.1",
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          "cdna_length": 4023,
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        },
        {
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            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 25,
          "intron_rank": 21,
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          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.3257-3131C>T",
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          "transcript": "XR_007064862.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_start": null,
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          "cdna_length": 5451,
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        },
        {
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            "intron_variant"
          ],
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          "exon_count": 27,
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          "gene_symbol": "RPGRIP1L",
          "gene_hgnc_id": 29168,
          "hgvs_c": "n.3371-3131C>T",
          "hgvs_p": null,
          "transcript": "XR_933260.4",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 4036,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "RPGRIP1L",
      "gene_hgnc_id": 29168,
      "dbsnp": "rs568801926",
      "frequency_reference_population": 0.0005230043,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 331,
      "gnomad_exomes_af": 0.000548316,
      "gnomad_genomes_af": 0.000442513,
      "gnomad_exomes_ac": 264,
      "gnomad_genomes_ac": 67,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.9200000166893005,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.92,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 0.229,
      "phylop100way_prediction": "Benign",
      "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": -6,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Strong,BP6,BP7",
      "acmg_by_gene": [
        {
          "score": -6,
          "benign_score": 6,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BP6",
            "BP7"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000647211.2",
          "gene_symbol": "RPGRIP1L",
          "hgnc_id": 29168,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.3312C>T",
          "hgvs_p": "p.Pro1104Pro"
        }
      ],
      "clinvar_disease": " type 5,Joubert syndrome,Joubert syndrome 7,Meckel syndrome,Meckel-Gruber syndrome,Nephronophthisis 8,not provided,not specified",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:3 LB:4",
      "phenotype_combined": "Nephronophthisis 8|not specified|Meckel syndrome, type 5|Joubert syndrome 7|not provided|Meckel-Gruber syndrome;Joubert syndrome",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}