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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: 19-38587418-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38587418&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "19",
      "pos": 38587418,
      "ref": "T",
      "alt": "A",
      "effect": "stop_lost",
      "transcript": "ENST00000359596.8",
      "consequences": [
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 106,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15115T>A",
          "hgvs_p": "p.Ter5039Argext*?",
          "transcript": "NM_000540.3",
          "protein_id": "NP_000531.2",
          "transcript_support_level": null,
          "aa_start": 5039,
          "aa_end": null,
          "aa_length": 5038,
          "cds_start": 15115,
          "cds_end": null,
          "cds_length": 15117,
          "cdna_start": 15254,
          "cdna_end": null,
          "cdna_length": 15400,
          "mane_select": "ENST00000359596.8",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 106,
          "exon_rank_end": null,
          "exon_count": 106,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15115T>A",
          "hgvs_p": "p.Ter5039Argext*?",
          "transcript": "ENST00000359596.8",
          "protein_id": "ENSP00000352608.2",
          "transcript_support_level": 5,
          "aa_start": 5039,
          "aa_end": null,
          "aa_length": 5038,
          "cds_start": 15115,
          "cds_end": null,
          "cds_length": 15117,
          "cdna_start": 15254,
          "cdna_end": null,
          "cdna_length": 15400,
          "mane_select": "NM_000540.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15100T>A",
          "hgvs_p": "p.Ter5034Argext*?",
          "transcript": "ENST00000355481.8",
          "protein_id": "ENSP00000347667.3",
          "transcript_support_level": 1,
          "aa_start": 5034,
          "aa_end": null,
          "aa_length": 5033,
          "cds_start": 15100,
          "cds_end": null,
          "cds_length": 15102,
          "cdna_start": 15231,
          "cdna_end": null,
          "cdna_length": 15377,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 103,
          "intron_rank": 102,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*5731+842T>A",
          "hgvs_p": null,
          "transcript": "ENST00000594335.6",
          "protein_id": "ENSP00000470927.2",
          "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": 15347,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15100T>A",
          "hgvs_p": "p.Ter5034Argext*?",
          "transcript": "NM_001042723.2",
          "protein_id": "NP_001036188.1",
          "transcript_support_level": null,
          "aa_start": 5034,
          "aa_end": null,
          "aa_length": 5033,
          "cds_start": 15100,
          "cds_end": null,
          "cds_length": 15102,
          "cdna_start": 15239,
          "cdna_end": null,
          "cdna_length": 15385,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15028T>A",
          "hgvs_p": "p.Ter5010Argext*?",
          "transcript": "ENST00000689936.2",
          "protein_id": "ENSP00000508999.2",
          "transcript_support_level": null,
          "aa_start": 5010,
          "aa_end": null,
          "aa_length": 5009,
          "cds_start": 15028,
          "cds_end": null,
          "cds_length": 15030,
          "cdna_start": 15167,
          "cdna_end": null,
          "cdna_length": 15169,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 104,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.14980T>A",
          "hgvs_p": "p.Ter4994Argext*?",
          "transcript": "ENST00000713953.1",
          "protein_id": "ENSP00000519246.1",
          "transcript_support_level": null,
          "aa_start": 4994,
          "aa_end": null,
          "aa_length": 4993,
          "cds_start": 14980,
          "cds_end": null,
          "cds_length": 14982,
          "cdna_start": 15111,
          "cdna_end": null,
          "cdna_length": 15257,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.14782T>A",
          "hgvs_p": "p.Ter4928Argext*?",
          "transcript": "ENST00000713952.1",
          "protein_id": "ENSP00000519245.1",
          "transcript_support_level": null,
          "aa_start": 4928,
          "aa_end": null,
          "aa_length": 4927,
          "cds_start": 14782,
          "cds_end": null,
          "cds_length": 14784,
          "cdna_start": 14921,
          "cdna_end": null,
          "cdna_length": 15067,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15097T>A",
          "hgvs_p": "p.Ter5033Argext*?",
          "transcript": "XM_006723317.3",
          "protein_id": "XP_006723380.1",
          "transcript_support_level": null,
          "aa_start": 5033,
          "aa_end": null,
          "aa_length": 5032,
          "cds_start": 15097,
          "cds_end": null,
          "cds_length": 15099,
          "cdna_start": 15236,
          "cdna_end": null,
          "cdna_length": 15382,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 104,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15082T>A",
          "hgvs_p": "p.Ter5028Argext*?",
          "transcript": "XM_006723319.3",
          "protein_id": "XP_006723382.1",
          "transcript_support_level": null,
          "aa_start": 5028,
          "aa_end": null,
          "aa_length": 5027,
          "cds_start": 15082,
          "cds_end": null,
          "cds_length": 15084,
          "cdna_start": 15221,
          "cdna_end": null,
          "cdna_length": 15367,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "c.15028T>A",
          "hgvs_p": "p.Ter5010Argext*?",
          "transcript": "XM_011527205.3",
          "protein_id": "XP_011525507.1",
          "transcript_support_level": null,
          "aa_start": 5010,
          "aa_end": null,
          "aa_length": 5009,
          "cds_start": 15028,
          "cds_end": null,
          "cds_length": 15030,
          "cdna_start": 15167,
          "cdna_end": null,
          "cdna_length": 15313,
          "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": 104,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*3485T>A",
          "hgvs_p": null,
          "transcript": "ENST00000593322.2",
          "protein_id": "ENSP00000471404.2",
          "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": 15308,
          "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": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*5874T>A",
          "hgvs_p": null,
          "transcript": "ENST00000599547.7",
          "protein_id": "ENSP00000471601.2",
          "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,
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          "cdna_length": 15200,
          "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": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*1370T>A",
          "hgvs_p": null,
          "transcript": "ENST00000688602.2",
          "protein_id": "ENSP00000510767.2",
          "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,
          "cdna_end": null,
          "cdna_length": 15322,
          "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": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.508T>A",
          "hgvs_p": null,
          "transcript": "ENST00000692547.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 654,
          "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": 104,
          "exon_rank_end": null,
          "exon_count": 104,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*3485T>A",
          "hgvs_p": null,
          "transcript": "ENST00000593322.2",
          "protein_id": "ENSP00000471404.2",
          "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,
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          "cdna_length": 15308,
          "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": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*5874T>A",
          "hgvs_p": null,
          "transcript": "ENST00000599547.7",
          "protein_id": "ENSP00000471601.2",
          "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": 15200,
          "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": 105,
          "exon_rank_end": null,
          "exon_count": 105,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RYR1",
          "gene_hgnc_id": 10483,
          "hgvs_c": "n.*1370T>A",
          "hgvs_p": null,
          "transcript": "ENST00000688602.2",
          "protein_id": "ENSP00000510767.2",
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MAP4K1",
          "gene_hgnc_id": 6863,
          "hgvs_c": "c.*330A>T",
          "hgvs_p": null,
          "transcript": "NM_001042600.3",
          "protein_id": "NP_001036065.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 821,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2466,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2631,
          "mane_select": "ENST00000396857.7",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 31,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MAP4K1",
          "gene_hgnc_id": 6863,
          "hgvs_c": "c.*330A>T",
          "hgvs_p": null,
          "transcript": "ENST00000396857.7",
          "protein_id": "ENSP00000380066.1",
          "transcript_support_level": 5,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 821,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": 2466,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2631,
          "mane_select": "NM_001042600.3",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 32,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MAP4K1",
          "gene_hgnc_id": 6863,
          "hgvs_c": "c.*392A>T",
          "hgvs_p": null,
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        },
        {
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          "consequences": [
            "downstream_gene_variant"
          ],
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          "exon_count": 32,
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          "gene_symbol": "MAP4K1",
          "gene_hgnc_id": 6863,
          "hgvs_c": "c.*330A>T",
          "hgvs_p": null,
          "transcript": "XM_011526404.2",
          "protein_id": "XP_011524706.1",
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          "aa_length": 861,
          "cds_start": -4,
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          "cds_length": 2586,
          "cdna_start": null,
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          "cdna_length": 2751,
          "mane_select": null,
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          "biotype": null,
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        }
      ],
      "gene_symbol": "RYR1",
      "gene_hgnc_id": 10483,
      "dbsnp": "rs1555806206",
      "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": 0.36000001430511475,
      "computational_prediction_selected": "Pathogenic",
      "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": 0.36,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 7.667,
      "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": 4,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PM4",
      "acmg_by_gene": [
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PM4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000359596.8",
          "gene_symbol": "RYR1",
          "hgnc_id": 10483,
          "effects": [
            "stop_lost"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.15115T>A",
          "hgvs_p": "p.Ter5039Argext*?"
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        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000396857.7",
          "gene_symbol": "MAP4K1",
          "hgnc_id": 6863,
          "effects": [
            "downstream_gene_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "c.*330A>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "RYR1-related disorder",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "RYR1-related disorder",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}