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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: 1-156139089-A-G (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=156139089&ref=A&alt=G&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 156139089,
      "ref": "A",
      "alt": "G",
      "effect": "missense_variant",
      "transcript": "ENST00000368300.9",
      "consequences": [
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "NM_170707.4",
          "protein_id": "NP_733821.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2186,
          "cdna_end": null,
          "cdna_length": 3178,
          "mane_select": "ENST00000368300.9",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "ENST00000368300.9",
          "protein_id": "ENSP00000357283.4",
          "transcript_support_level": 1,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2186,
          "cdna_end": null,
          "cdna_length": 3178,
          "mane_select": "NM_170707.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1828A>G",
          "hgvs_p": "p.Asn610Asp",
          "transcript": "ENST00000368299.7",
          "protein_id": "ENSP00000357282.3",
          "transcript_support_level": 1,
          "aa_start": 610,
          "aa_end": null,
          "aa_length": 614,
          "cds_start": 1828,
          "cds_end": null,
          "cds_length": 1845,
          "cdna_start": 2025,
          "cdna_end": null,
          "cdna_length": 2253,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "NM_001406985.1",
          "protein_id": "NP_001393914.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 686,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 2061,
          "cdna_start": 2186,
          "cdna_end": null,
          "cdna_length": 2511,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 14,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "NM_001406983.1",
          "protein_id": "NP_001393912.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2512,
          "cdna_end": null,
          "cdna_length": 3504,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "NM_001406991.1",
          "protein_id": "NP_001393920.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2292,
          "cdna_end": null,
          "cdna_length": 3284,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "ENST00000361308.9",
          "protein_id": "ENSP00000355292.6",
          "transcript_support_level": 5,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2261,
          "cdna_end": null,
          "cdna_length": 2465,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "ENST00000675939.1",
          "protein_id": "ENSP00000502256.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2197,
          "cdna_end": null,
          "cdna_length": 2401,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp",
          "transcript": "ENST00000683032.1",
          "protein_id": "ENSP00000506771.1",
          "transcript_support_level": null,
          "aa_start": 660,
          "aa_end": null,
          "aa_length": 664,
          "cds_start": 1978,
          "cds_end": null,
          "cds_length": 1995,
          "cdna_start": 2193,
          "cdna_end": null,
          "cdna_length": 2329,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1888A>G",
          "hgvs_p": "p.Asn630Asp",
          "transcript": "NM_170708.4",
          "protein_id": "NP_733822.1",
          "transcript_support_level": null,
          "aa_start": 630,
          "aa_end": null,
          "aa_length": 634,
          "cds_start": 1888,
          "cds_end": null,
          "cds_length": 1905,
          "cdna_start": 2096,
          "cdna_end": null,
          "cdna_length": 3088,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 13,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1888A>G",
          "hgvs_p": "p.Asn630Asp",
          "transcript": "ENST00000676385.2",
          "protein_id": "ENSP00000502091.1",
          "transcript_support_level": null,
          "aa_start": 630,
          "aa_end": null,
          "aa_length": 634,
          "cds_start": 1888,
          "cds_end": null,
          "cds_length": 1905,
          "cdna_start": 2729,
          "cdna_end": null,
          "cdna_length": 2811,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1888A>G",
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          "transcript": "ENST00000682650.1",
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          "cdna_start": 2102,
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          "mane_select": null,
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        },
        {
          "aa_ref": "N",
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          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 12,
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
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          "hgvs_c": "c.1828A>G",
          "hgvs_p": "p.Asn610Asp",
          "transcript": "NM_001282626.2",
          "protein_id": "NP_001269555.1",
          "transcript_support_level": null,
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          "cds_start": 1828,
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          "cdna_start": 2036,
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        {
          "aa_ref": "N",
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 13,
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          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1735A>G",
          "hgvs_p": "p.Asn579Asp",
          "transcript": "NM_001406986.1",
          "protein_id": "NP_001393915.1",
          "transcript_support_level": null,
          "aa_start": 579,
          "aa_end": null,
          "aa_length": 583,
          "cds_start": 1735,
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          "cds_length": 1752,
          "cdna_start": 2366,
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          "cdna_length": 3358,
          "mane_select": null,
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          "feature": null
        },
        {
          "aa_ref": "N",
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "LMNA",
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          "hgvs_c": "c.1735A>G",
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          "transcript": "NM_001406987.1",
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        },
        {
          "aa_ref": "N",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 12,
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          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1642A>G",
          "hgvs_p": "p.Asn548Asp",
          "transcript": "NM_001257374.3",
          "protein_id": "NP_001244303.1",
          "transcript_support_level": null,
          "aa_start": 548,
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          "aa_length": 574,
          "cds_start": 1642,
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          "mane_select": null,
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        },
        {
          "aa_ref": "N",
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          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 12,
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          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1642A>G",
          "hgvs_p": "p.Asn548Asp",
          "transcript": "ENST00000448611.6",
          "protein_id": "ENSP00000395597.2",
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          "aa_end": null,
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          "cds_start": 1642,
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          "cdna_start": 1686,
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        },
        {
          "aa_ref": "N",
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          "strand": true,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1681A>G",
          "hgvs_p": "p.Asn561Asp",
          "transcript": "NM_001406988.1",
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        {
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          ],
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          "exon_count": 13,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1681A>G",
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        },
        {
          "aa_ref": "N",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          "exon_count": 12,
          "intron_rank": null,
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          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
          "hgvs_c": "c.1642A>G",
          "hgvs_p": "p.Asn548Asp",
          "transcript": "NM_001406989.1",
          "protein_id": "NP_001393918.1",
          "transcript_support_level": null,
          "aa_start": 548,
          "aa_end": null,
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          "cds_start": 1642,
          "cds_end": null,
          "cds_length": 1659,
          "cdna_start": 1676,
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          "cdna_length": 2668,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "N",
          "aa_alt": "D",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "LMNA",
          "gene_hgnc_id": 6636,
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        },
        {
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          ],
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          "gene_symbol": "LMNA",
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          "hgvs_c": "n.163+482A>G",
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        },
        {
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          "protein_coding": false,
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          "consequences": [
            "downstream_gene_variant"
          ],
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          "exon_count": 11,
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          "gene_symbol": "LMNA",
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          "hgvs_c": "n.*2055A>G",
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          "transcript": "ENST00000676434.1",
          "protein_id": "ENSP00000501648.1",
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          "cdna_start": null,
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          "cdna_length": 3212,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        }
      ],
      "gene_symbol": "LMNA",
      "gene_hgnc_id": 6636,
      "dbsnp": "rs374926367",
      "frequency_reference_population": 0.000091102906,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 147,
      "gnomad_exomes_af": 0.0000902993,
      "gnomad_genomes_af": 0.0000988442,
      "gnomad_exomes_ac": 132,
      "gnomad_genomes_ac": 15,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.011655736714601517,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "CardioboostCm",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.305,
      "revel_prediction": "Uncertain_significance",
      "alphamissense_score": 0.2015,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.11,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 4.351,
      "phylop100way_prediction": "Uncertain_significance",
      "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": -2,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "BP4_Moderate",
      "acmg_by_gene": [
        {
          "score": -2,
          "benign_score": 2,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Moderate"
          ],
          "verdict": "Likely_benign",
          "transcript": "ENST00000368300.9",
          "gene_symbol": "LMNA",
          "hgnc_id": 6636,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD,AR,SD",
          "hgvs_c": "c.1978A>G",
          "hgvs_p": "p.Asn660Asp"
        }
      ],
      "clinvar_disease": "11 conditions,Cardiomyopathy,Cardiovascular phenotype,Charcot-Marie-Tooth disease type 2,Primary dilated cardiomyopathy,not provided",
      "clinvar_classification": "Conflicting classifications of pathogenicity",
      "clinvar_review_status": "criteria provided, conflicting classifications",
      "clinvar_submissions_summary": "US:9 LB:1",
      "phenotype_combined": "not provided|Cardiomyopathy|Charcot-Marie-Tooth disease type 2|11 conditions|Cardiovascular phenotype|Primary dilated cardiomyopathy",
      "pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
      "custom_annotations": null
    }
  ],
  "message": null
}