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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: 1-161213726-C-T (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=161213726&ref=C&alt=T&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 161213726,
      "ref": "C",
      "alt": "T",
      "effect": "synonymous_variant",
      "transcript": "ENST00000676972.1",
      "consequences": [
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001377299.1",
          "protein_id": "NP_001364228.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1309,
          "cdna_end": null,
          "cdna_length": 1613,
          "mane_select": "ENST00000676972.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000676972.1",
          "protein_id": "ENSP00000503117.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1309,
          "cdna_end": null,
          "cdna_length": 1613,
          "mane_select": "NM_001377299.1",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000367993.7",
          "protein_id": "ENSP00000356972.3",
          "transcript_support_level": 1,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1738,
          "cdna_end": null,
          "cdna_length": 2042,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000392179.5",
          "protein_id": "ENSP00000376018.4",
          "transcript_support_level": 1,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 457,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1374,
          "cdna_start": 1529,
          "cdna_end": null,
          "cdna_length": 2067,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1353C>T",
          "hgvs_p": "p.Ala451Ala",
          "transcript": "ENST00000677453.1",
          "protein_id": "ENSP00000503604.1",
          "transcript_support_level": null,
          "aa_start": 451,
          "aa_end": null,
          "aa_length": 484,
          "cds_start": 1353,
          "cds_end": null,
          "cds_length": 1455,
          "cdna_start": 1469,
          "cdna_end": null,
          "cdna_length": 1889,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1353C>T",
          "hgvs_p": "p.Ala451Ala",
          "transcript": "ENST00000677846.1",
          "protein_id": "ENSP00000504065.1",
          "transcript_support_level": null,
          "aa_start": 451,
          "aa_end": null,
          "aa_length": 484,
          "cds_start": 1353,
          "cds_end": null,
          "cds_length": 1455,
          "cdna_start": 1656,
          "cdna_end": null,
          "cdna_length": 1939,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1353C>T",
          "hgvs_p": "p.Ala451Ala",
          "transcript": "ENST00000677579.1",
          "protein_id": "ENSP00000504162.1",
          "transcript_support_level": null,
          "aa_start": 451,
          "aa_end": null,
          "aa_length": 478,
          "cds_start": 1353,
          "cds_end": null,
          "cds_length": 1437,
          "cdna_start": 1656,
          "cdna_end": null,
          "cdna_length": 2092,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001377298.1",
          "protein_id": "NP_001364227.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1600,
          "cdna_end": null,
          "cdna_length": 1904,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_004550.5",
          "protein_id": "NP_004541.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1738,
          "cdna_end": null,
          "cdna_length": 2042,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000676600.1",
          "protein_id": "ENSP00000503989.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1456,
          "cdna_end": null,
          "cdna_length": 1746,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000678507.1",
          "protein_id": "ENSP00000504199.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
          "cds_end": null,
          "cds_length": 1392,
          "cdna_start": 1601,
          "cdna_end": null,
          "cdna_length": 1891,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 15,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000678511.1",
          "protein_id": "ENSP00000504846.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 463,
          "cds_start": 1290,
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          "cds_length": 1392,
          "cdna_start": 1376,
          "cdna_end": null,
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          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001166159.2",
          "protein_id": "NP_001159631.1",
          "transcript_support_level": null,
          "aa_start": 430,
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          "aa_length": 457,
          "cds_start": 1290,
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          "cdna_start": 1309,
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          "cdna_length": 1847,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001377300.1",
          "protein_id": "NP_001364229.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 457,
          "cds_start": 1290,
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          "cds_length": 1374,
          "cdna_start": 1600,
          "cdna_end": null,
          "cdna_length": 2138,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001377301.1",
          "protein_id": "NP_001364230.1",
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          "cds_start": 1290,
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          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
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          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "NM_001377302.1",
          "protein_id": "NP_001364231.1",
          "transcript_support_level": null,
          "aa_start": 430,
          "aa_end": null,
          "aa_length": 457,
          "cds_start": 1290,
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          "cdna_start": 1309,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 13,
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          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000677550.1",
          "protein_id": "ENSP00000503353.1",
          "transcript_support_level": null,
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          "cds_start": 1290,
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          "cdna_start": 1645,
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          "cdna_length": 2169,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 13,
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          "intron_rank": null,
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          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala",
          "transcript": "ENST00000679176.1",
          "protein_id": "ENSP00000504170.1",
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        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
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          "intron_rank": null,
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          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1215C>T",
          "hgvs_p": "p.Ala405Ala",
          "transcript": "ENST00000678783.1",
          "protein_id": "ENSP00000504215.1",
          "transcript_support_level": null,
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          "cdna_start": 1314,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
          "gene_hgnc_id": 7708,
          "hgvs_c": "c.1212C>T",
          "hgvs_p": "p.Ala404Ala",
          "transcript": "NM_001410889.1",
          "protein_id": "NP_001397818.1",
          "transcript_support_level": null,
          "aa_start": 404,
          "aa_end": null,
          "aa_length": 437,
          "cds_start": 1212,
          "cds_end": null,
          "cds_length": 1314,
          "cdna_start": 1231,
          "cdna_end": null,
          "cdna_length": 1535,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "A",
          "aa_alt": "A",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NDUFS2",
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        {
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          "gene_symbol": "NDUFS2",
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          "transcript": "ENST00000679282.1",
          "protein_id": "ENSP00000504533.1",
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          "cdna_length": 1709,
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        }
      ],
      "gene_symbol": "NDUFS2",
      "gene_hgnc_id": 7708,
      "dbsnp": "rs1136207",
      "frequency_reference_population": 0.13787958,
      "hom_count_reference_population": 17249,
      "allele_count_reference_population": 222520,
      "gnomad_exomes_af": 0.139394,
      "gnomad_genomes_af": 0.123329,
      "gnomad_exomes_ac": 203756,
      "gnomad_genomes_ac": 18764,
      "gnomad_exomes_homalt": 15781,
      "gnomad_genomes_homalt": 1468,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.25,
      "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": -0.25,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.57,
      "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": -19,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
      "acmg_by_gene": [
        {
          "score": -19,
          "benign_score": 19,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate",
            "BP6_Very_Strong",
            "BP7",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000676972.1",
          "gene_symbol": "NDUFS2",
          "hgnc_id": 7708,
          "effects": [
            "synonymous_variant"
          ],
          "inheritance_mode": "AR,Mitochondrial,Unknown",
          "hgvs_c": "c.1290C>T",
          "hgvs_p": "p.Ala430Ala"
        }
      ],
      "clinvar_disease": " nuclear type 1, nuclear type 6,Mitochondrial complex I deficiency,not provided,not specified",
      "clinvar_classification": "Benign",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "B:5",
      "phenotype_combined": "not specified|Mitochondrial complex I deficiency, nuclear type 1|not provided|Mitochondrial complex I deficiency, nuclear type 6",
      "pathogenicity_classification_combined": "Benign",
      "custom_annotations": null
    }
  ],
  "message": null
}