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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: 2-178834364-T-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=178834364&ref=T&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "2",
      "pos": 178834364,
      "ref": "T",
      "alt": "A",
      "effect": "missense_variant",
      "transcript": "NM_173648.4",
      "consequences": [
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "NM_173648.4",
          "protein_id": "NP_775919.3",
          "transcript_support_level": null,
          "aa_start": 1468,
          "aa_end": null,
          "aa_length": 1530,
          "cds_start": 4402,
          "cds_end": null,
          "cds_length": 4593,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000443758.7",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_173648.4"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "ENST00000443758.7",
          "protein_id": "ENSP00000390190.2",
          "transcript_support_level": 5,
          "aa_start": 1468,
          "aa_end": null,
          "aa_length": 1530,
          "cds_start": 4402,
          "cds_end": null,
          "cds_length": 4593,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_173648.4",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000443758.7"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "ENST00000922698.1",
          "protein_id": "ENSP00000592757.1",
          "transcript_support_level": null,
          "aa_start": 1468,
          "aa_end": null,
          "aa_length": 1530,
          "cds_start": 4402,
          "cds_end": null,
          "cds_length": 4593,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000922698.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 23,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4222A>T",
          "hgvs_p": "p.Ile1408Phe",
          "transcript": "ENST00000894515.1",
          "protein_id": "ENSP00000564574.1",
          "transcript_support_level": null,
          "aa_start": 1408,
          "aa_end": null,
          "aa_length": 1470,
          "cds_start": 4222,
          "cds_end": null,
          "cds_length": 4413,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000894515.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4619A>T",
          "hgvs_p": "p.His1540Leu",
          "transcript": "XM_011510991.4",
          "protein_id": "XP_011509293.1",
          "transcript_support_level": null,
          "aa_start": 1540,
          "aa_end": null,
          "aa_length": 1558,
          "cds_start": 4619,
          "cds_end": null,
          "cds_length": 4677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_011510991.4"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4619A>T",
          "hgvs_p": "p.His1540Leu",
          "transcript": "XM_047443983.1",
          "protein_id": "XP_047299939.1",
          "transcript_support_level": null,
          "aa_start": 1540,
          "aa_end": null,
          "aa_length": 1558,
          "cds_start": 4619,
          "cds_end": null,
          "cds_length": 4677,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443983.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 25,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4616A>T",
          "hgvs_p": "p.His1539Leu",
          "transcript": "XM_047443984.1",
          "protein_id": "XP_047299940.1",
          "transcript_support_level": null,
          "aa_start": 1539,
          "aa_end": null,
          "aa_length": 1557,
          "cds_start": 4616,
          "cds_end": null,
          "cds_length": 4674,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443984.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4619A>T",
          "hgvs_p": "p.His1540Leu",
          "transcript": "XM_011510992.4",
          "protein_id": "XP_011509294.1",
          "transcript_support_level": null,
          "aa_start": 1540,
          "aa_end": null,
          "aa_length": 1554,
          "cds_start": 4619,
          "cds_end": null,
          "cds_length": 4665,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_011510992.4"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4619A>T",
          "hgvs_p": "p.His1540Leu",
          "transcript": "XM_047443985.1",
          "protein_id": "XP_047299941.1",
          "transcript_support_level": null,
          "aa_start": 1540,
          "aa_end": null,
          "aa_length": 1554,
          "cds_start": 4619,
          "cds_end": null,
          "cds_length": 4665,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443985.1"
        },
        {
          "aa_ref": "H",
          "aa_alt": "L",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 25,
          "exon_rank_end": null,
          "exon_count": 30,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4619A>T",
          "hgvs_p": "p.His1540Leu",
          "transcript": "XM_047443986.1",
          "protein_id": "XP_047299942.1",
          "transcript_support_level": null,
          "aa_start": 1540,
          "aa_end": null,
          "aa_length": 1554,
          "cds_start": 4619,
          "cds_end": null,
          "cds_length": 4665,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443986.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4399A>T",
          "hgvs_p": "p.Ile1467Phe",
          "transcript": "XM_047443987.1",
          "protein_id": "XP_047299943.1",
          "transcript_support_level": null,
          "aa_start": 1467,
          "aa_end": null,
          "aa_length": 1529,
          "cds_start": 4399,
          "cds_end": null,
          "cds_length": 4590,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443987.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443988.1",
          "protein_id": "XP_047299944.1",
          "transcript_support_level": null,
          "aa_start": 1468,
          "aa_end": null,
          "aa_length": 1511,
          "cds_start": 4402,
          "cds_end": null,
          "cds_length": 4536,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443988.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443989.1",
          "protein_id": "XP_047299945.1",
          "transcript_support_level": null,
          "aa_start": 1468,
          "aa_end": null,
          "aa_length": 1511,
          "cds_start": 4402,
          "cds_end": null,
          "cds_length": 4536,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443989.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 26,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443990.1",
          "protein_id": "XP_047299946.1",
          "transcript_support_level": null,
          "aa_start": 1468,
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          "aa_length": 1511,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "H",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
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          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4439A>T",
          "hgvs_p": "p.His1480Leu",
          "transcript": "XM_047443991.1",
          "protein_id": "XP_047299947.1",
          "transcript_support_level": null,
          "aa_start": 1480,
          "aa_end": null,
          "aa_length": 1498,
          "cds_start": 4439,
          "cds_end": null,
          "cds_length": 4497,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "XM_047443991.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 28,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443992.1",
          "protein_id": "XP_047299948.1",
          "transcript_support_level": null,
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          "aa_end": null,
          "aa_length": 1472,
          "cds_start": 4402,
          "cds_end": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_047443992.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443993.1",
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        {
          "aa_ref": "I",
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          "canonical": false,
          "protein_coding": true,
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          ],
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          "intron_rank": null,
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          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443994.1",
          "protein_id": "XP_047299950.1",
          "transcript_support_level": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "I",
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          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
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          "exon_count": 26,
          "intron_rank": null,
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          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
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          "transcript": "XM_047443995.1",
          "protein_id": "XP_047299951.1",
          "transcript_support_level": null,
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          "cds_start": 4402,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "XM_047443995.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "F",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 24,
          "exon_rank_end": null,
          "exon_count": 29,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "CCDC141",
          "gene_hgnc_id": 26821,
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe",
          "transcript": "XM_047443996.1",
          "protein_id": "XP_047299952.1",
          "transcript_support_level": null,
          "aa_start": 1468,
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        {
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          ],
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          "gene_symbol": "ENSG00000287149",
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        {
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          "gene_symbol": "ENSG00000287149",
          "gene_hgnc_id": null,
          "hgvs_c": "n.293+5710T>A",
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          "transcript": "ENST00000846150.1",
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          "cds_length": null,
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          "biotype": "pseudogene",
          "feature": "ENST00000846150.1"
        }
      ],
      "gene_symbol": "CCDC141",
      "gene_hgnc_id": 26821,
      "dbsnp": null,
      "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": 0.914249062538147,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.686,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.3507,
      "alphamissense_prediction": "Uncertain_significance",
      "bayesdelnoaf_score": -0.13,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 6.327,
      "phylop100way_prediction": "Uncertain_significance",
      "spliceai_max_score": 0.01,
      "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,PP3_Moderate",
      "acmg_by_gene": [
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_173648.4",
          "gene_symbol": "CCDC141",
          "hgnc_id": 26821,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.4402A>T",
          "hgvs_p": "p.Ile1468Phe"
        },
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PP3_Moderate"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "ENST00000846151.1",
          "gene_symbol": "ENSG00000287149",
          "hgnc_id": null,
          "effects": [
            "non_coding_transcript_exon_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.204T>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}