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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: 6-131949382-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131949382&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "6",
      "pos": 131949382,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_001901.4",
      "consequences": [
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.932A>G",
          "hgvs_p": "p.Glu311Gly",
          "transcript": "NM_001901.4",
          "protein_id": "NP_001892.2",
          "transcript_support_level": null,
          "aa_start": 311,
          "aa_end": null,
          "aa_length": 349,
          "cds_start": 932,
          "cds_end": null,
          "cds_length": 1050,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000367976.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001901.4"
        },
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.932A>G",
          "hgvs_p": "p.Glu311Gly",
          "transcript": "ENST00000367976.4",
          "protein_id": "ENSP00000356954.3",
          "transcript_support_level": 1,
          "aa_start": 311,
          "aa_end": null,
          "aa_length": 349,
          "cds_start": 932,
          "cds_end": null,
          "cds_length": 1050,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_001901.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000367976.4"
        },
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.929A>G",
          "hgvs_p": "p.Glu310Gly",
          "transcript": "ENST00000873798.1",
          "protein_id": "ENSP00000543857.1",
          "transcript_support_level": null,
          "aa_start": 310,
          "aa_end": null,
          "aa_length": 348,
          "cds_start": 929,
          "cds_end": null,
          "cds_length": 1047,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000873798.1"
        },
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.926A>G",
          "hgvs_p": "p.Glu309Gly",
          "transcript": "ENST00000918595.1",
          "protein_id": "ENSP00000588654.1",
          "transcript_support_level": null,
          "aa_start": 309,
          "aa_end": null,
          "aa_length": 347,
          "cds_start": 926,
          "cds_end": null,
          "cds_length": 1044,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000918595.1"
        },
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.809A>G",
          "hgvs_p": "p.Glu270Gly",
          "transcript": "ENST00000918596.1",
          "protein_id": "ENSP00000588655.1",
          "transcript_support_level": null,
          "aa_start": 270,
          "aa_end": null,
          "aa_length": 308,
          "cds_start": 809,
          "cds_end": null,
          "cds_length": 927,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000918596.1"
        },
        {
          "aa_ref": "E",
          "aa_alt": "G",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCN2",
          "gene_hgnc_id": 2500,
          "hgvs_c": "c.680A>G",
          "hgvs_p": "p.Glu227Gly",
          "transcript": "ENST00000918594.1",
          "protein_id": "ENSP00000588653.1",
          "transcript_support_level": null,
          "aa_start": 227,
          "aa_end": null,
          "aa_length": 265,
          "cds_start": 680,
          "cds_end": null,
          "cds_length": 798,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000918594.1"
        },
        {
          "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": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.182+47231T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706294.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000706294.2"
        },
        {
          "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": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.239+47231T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706326.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000706326.1"
        },
        {
          "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": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.559+45148T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706327.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000706327.1"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.342+25312T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706328.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000706328.1"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.471-29031T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706330.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000706330.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 3,
          "intron_rank": 1,
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          "gene_symbol": "LINC01013",
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          "hgvs_c": "n.87+47231T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706331.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "pseudogene",
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        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
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          ],
          "exon_rank": null,
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          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.431+25312T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706350.1",
          "protein_id": null,
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          "cds_start": null,
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        },
        {
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          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "intron_rank": 2,
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          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.419+38427T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706351.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "aa_length": null,
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        },
        {
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          ],
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          "biotype": "pseudogene",
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
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          ],
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          "intron_rank": 2,
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          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.187+25312T>C",
          "hgvs_p": null,
          "transcript": "ENST00000706353.1",
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        {
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          "canonical": false,
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          ],
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          "gene_symbol": "LINC01013",
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          "hgvs_c": "n.231+25312T>C",
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          "feature": "ENST00000706354.1"
        },
        {
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          "strand": true,
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          "gene_symbol": "LINC01013",
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        {
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          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.220-29264T>C",
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        },
        {
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          "strand": true,
          "consequences": [
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          ],
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          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.309+25312T>C",
          "hgvs_p": null,
          "transcript": "ENST00000773265.1",
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "ENST00000773265.1"
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "LINC01013",
          "gene_hgnc_id": 48987,
          "hgvs_c": "n.198+38427T>C",
          "hgvs_p": null,
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        {
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          "protein_coding": false,
          "strand": true,
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          "intron_rank": 2,
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        {
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          "strand": true,
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          "exon_count": 4,
          "intron_rank": 2,
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          "gene_symbol": "CCN2-AS1",
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          "hgvs_c": "n.488+45148T>C",
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          "mane_select": null,
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        },
        {
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          "protein_coding": false,
          "strand": true,
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          ],
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          "exon_count": 6,
          "intron_rank": 2,
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          "gene_symbol": "CCN2-AS1",
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          "hgvs_c": "n.327+25312T>C",
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          "transcript": "NR_187595.1",
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          "biotype": "pseudogene",
          "feature": "NR_187595.1"
        },
        {
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          ],
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          "exon_count": 3,
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          "gene_symbol": "CCN2-AS1",
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          "hgvs_c": "n.488+45148T>C",
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          "transcript": "NR_187596.1",
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "pseudogene",
          "feature": "NR_187596.1"
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      ],
      "gene_symbol": "CCN2",
      "gene_hgnc_id": 2500,
      "dbsnp": "rs141716795",
      "frequency_reference_population": 0.0002323302,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 375,
      "gnomad_exomes_af": 0.000238048,
      "gnomad_genomes_af": 0.000177407,
      "gnomad_exomes_ac": 348,
      "gnomad_genomes_ac": 27,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.3346279263496399,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.175,
      "revel_prediction": "Benign",
      "alphamissense_score": 0.2392,
      "alphamissense_prediction": "Benign",
      "bayesdelnoaf_score": -0.38,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 8.017,
      "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": -1,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4",
      "acmg_by_gene": [
        {
          "score": -1,
          "benign_score": 1,
          "pathogenic_score": 0,
          "criteria": [
            "BP4"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_001901.4",
          "gene_symbol": "CCN2",
          "hgnc_id": 2500,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AR,AD",
          "hgvs_c": "c.932A>G",
          "hgvs_p": "p.Glu311Gly"
        },
        {
          "score": -1,
          "benign_score": 1,
          "pathogenic_score": 0,
          "criteria": [
            "BP4"
          ],
          "verdict": "Likely_benign",
          "transcript": "NR_187593.1",
          "gene_symbol": "CCN2-AS1",
          "hgnc_id": 40164,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.371+38427T>C",
          "hgvs_p": null
        },
        {
          "score": -1,
          "benign_score": 1,
          "pathogenic_score": 0,
          "criteria": [
            "BP4"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000706294.2",
          "gene_symbol": "LINC01013",
          "hgnc_id": 48987,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.182+47231T>C",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not specified",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not specified",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}