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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: 3-12585760-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=12585760&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 12585760,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "ENST00000251849.9",
      "consequences": [
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly",
          "transcript": "NM_002880.4",
          "protein_id": "NP_002871.1",
          "transcript_support_level": null,
          "aa_start": 486,
          "aa_end": null,
          "aa_length": 648,
          "cds_start": 1457,
          "cds_end": null,
          "cds_length": 1947,
          "cdna_start": 1788,
          "cdna_end": null,
          "cdna_length": 3191,
          "mane_select": "ENST00000251849.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly",
          "transcript": "ENST00000251849.9",
          "protein_id": "ENSP00000251849.4",
          "transcript_support_level": 1,
          "aa_start": 486,
          "aa_end": null,
          "aa_length": 648,
          "cds_start": 1457,
          "cds_end": null,
          "cds_length": 1947,
          "cdna_start": 1788,
          "cdna_end": null,
          "cdna_length": 3191,
          "mane_select": "NM_002880.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1517A>G",
          "hgvs_p": "p.Asp506Gly",
          "transcript": "NM_001354689.3",
          "protein_id": "NP_001341618.1",
          "transcript_support_level": null,
          "aa_start": 506,
          "aa_end": null,
          "aa_length": 668,
          "cds_start": 1517,
          "cds_end": null,
          "cds_length": 2007,
          "cdna_start": 1848,
          "cdna_end": null,
          "cdna_length": 3251,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 15,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1517A>G",
          "hgvs_p": "p.Asp506Gly",
          "transcript": "ENST00000442415.7",
          "protein_id": "ENSP00000401888.2",
          "transcript_support_level": 5,
          "aa_start": 506,
          "aa_end": null,
          "aa_length": 668,
          "cds_start": 1517,
          "cds_end": null,
          "cds_length": 2007,
          "cdna_start": 1848,
          "cdna_end": null,
          "cdna_length": 3251,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly",
          "transcript": "NM_001354690.3",
          "protein_id": "NP_001341619.1",
          "transcript_support_level": null,
          "aa_start": 486,
          "aa_end": null,
          "aa_length": 648,
          "cds_start": 1457,
          "cds_end": null,
          "cds_length": 1947,
          "cdna_start": 1623,
          "cdna_end": null,
          "cdna_length": 3026,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly",
          "transcript": "ENST00000685653.1",
          "protein_id": "ENSP00000509968.1",
          "transcript_support_level": null,
          "aa_start": 486,
          "aa_end": null,
          "aa_length": 648,
          "cds_start": 1457,
          "cds_end": null,
          "cds_length": 1947,
          "cdna_start": 3162,
          "cdna_end": null,
          "cdna_length": 4402,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly",
          "transcript": "ENST00000691899.1",
          "protein_id": "ENSP00000508763.1",
          "transcript_support_level": null,
          "aa_start": 486,
          "aa_end": null,
          "aa_length": 648,
          "cds_start": 1457,
          "cds_end": null,
          "cds_length": 1947,
          "cdna_start": 1623,
          "cdna_end": null,
          "cdna_length": 2983,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1445A>G",
          "hgvs_p": "p.Asp482Gly",
          "transcript": "ENST00000690460.1",
          "protein_id": "ENSP00000509106.1",
          "transcript_support_level": null,
          "aa_start": 482,
          "aa_end": null,
          "aa_length": 644,
          "cds_start": 1445,
          "cds_end": null,
          "cds_length": 1935,
          "cdna_start": 1776,
          "cdna_end": null,
          "cdna_length": 3141,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1358A>G",
          "hgvs_p": "p.Asp453Gly",
          "transcript": "NM_001354693.3",
          "protein_id": "NP_001341622.1",
          "transcript_support_level": null,
          "aa_start": 453,
          "aa_end": null,
          "aa_length": 615,
          "cds_start": 1358,
          "cds_end": null,
          "cds_length": 1848,
          "cdna_start": 1689,
          "cdna_end": null,
          "cdna_length": 3092,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1358A>G",
          "hgvs_p": "p.Asp453Gly",
          "transcript": "ENST00000685437.1",
          "protein_id": "ENSP00000508794.1",
          "transcript_support_level": null,
          "aa_start": 453,
          "aa_end": null,
          "aa_length": 615,
          "cds_start": 1358,
          "cds_end": null,
          "cds_length": 1848,
          "cdna_start": 1782,
          "cdna_end": null,
          "cdna_length": 2866,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1358A>G",
          "hgvs_p": "p.Asp453Gly",
          "transcript": "ENST00000688543.1",
          "protein_id": "ENSP00000509612.1",
          "transcript_support_level": null,
          "aa_start": 453,
          "aa_end": null,
          "aa_length": 615,
          "cds_start": 1358,
          "cds_end": null,
          "cds_length": 1848,
          "cdna_start": 1759,
          "cdna_end": null,
          "cdna_length": 4662,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1358A>G",
          "hgvs_p": "p.Asp453Gly",
          "transcript": "ENST00000692093.1",
          "protein_id": "ENSP00000509669.1",
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          "cds_start": 1358,
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          "cdna_start": 1791,
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          "cdna_length": 3187,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1346A>G",
          "hgvs_p": "p.Asp449Gly",
          "transcript": "ENST00000687923.1",
          "protein_id": "ENSP00000510255.1",
          "transcript_support_level": null,
          "aa_start": 449,
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          "cds_start": 1346,
          "cds_end": null,
          "cds_length": 1836,
          "cdna_start": 1671,
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          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1346A>G",
          "hgvs_p": "p.Asp449Gly",
          "transcript": "ENST00000690397.1",
          "protein_id": "ENSP00000508730.1",
          "transcript_support_level": null,
          "aa_start": 449,
          "aa_end": null,
          "aa_length": 611,
          "cds_start": 1346,
          "cds_end": null,
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          "cdna_start": 1677,
          "cdna_end": null,
          "cdna_length": 3037,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1280A>G",
          "hgvs_p": "p.Asp427Gly",
          "transcript": "ENST00000689389.1",
          "protein_id": "ENSP00000510213.1",
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          "cdna_start": 1614,
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          "mane_select": null,
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          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 14,
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          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1274A>G",
          "hgvs_p": "p.Asp425Gly",
          "transcript": "NM_001354694.3",
          "protein_id": "NP_001341623.1",
          "transcript_support_level": null,
          "aa_start": 425,
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          "cds_start": 1274,
          "cds_end": null,
          "cds_length": 1764,
          "cdna_start": 1735,
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          "cdna_length": 3138,
          "mane_select": null,
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        },
        {
          "aa_ref": "D",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1232A>G",
          "hgvs_p": "p.Asp411Gly",
          "transcript": "ENST00000693312.1",
          "protein_id": "ENSP00000508686.1",
          "transcript_support_level": null,
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          "aa_length": 573,
          "cds_start": 1232,
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          "cdna_start": 1533,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
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          "intron_rank": null,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1214A>G",
          "hgvs_p": "p.Asp405Gly",
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          "protein_id": "NP_001341620.1",
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        },
        {
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
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          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1214A>G",
          "hgvs_p": "p.Asp405Gly",
          "transcript": "NM_001354692.3",
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          "cdna_length": 3078,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
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          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.1115A>G",
          "hgvs_p": "p.Asp372Gly",
          "transcript": "NM_001354695.3",
          "protein_id": "NP_001341624.1",
          "transcript_support_level": null,
          "aa_start": 372,
          "aa_end": null,
          "aa_length": 534,
          "cds_start": 1115,
          "cds_end": null,
          "cds_length": 1605,
          "cdna_start": 1576,
          "cdna_end": null,
          "cdna_length": 2979,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "D",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 8,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "RAF1",
          "gene_hgnc_id": 9829,
          "hgvs_c": "c.773A>G",
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      "gene_hgnc_id": 9829,
      "dbsnp": "rs397516815",
      "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": 0.9918049573898315,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.987,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9999,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.59,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 8.012,
      "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": 16,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PM1,PM2,PP3_Strong,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 16,
          "benign_score": 0,
          "pathogenic_score": 16,
          "criteria": [
            "PM1",
            "PM2",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000251849.9",
          "gene_symbol": "RAF1",
          "hgnc_id": 9829,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.1457A>G",
          "hgvs_p": "p.Asp486Gly"
        },
        {
          "score": 14,
          "benign_score": 0,
          "pathogenic_score": 14,
          "criteria": [
            "PM2",
            "PP3_Strong",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000677816.1",
          "gene_symbol": "MKRN2",
          "hgnc_id": 7113,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "n.*2062T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "Noonan syndrome,RAF1-related disorder,RASopathy,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:4 LP:1",
      "phenotype_combined": "Noonan syndrome|not provided|RASopathy|RAF1-related disorder",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}