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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: 4-87657075-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=87657075&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "4",
      "pos": 87657075,
      "ref": "G",
      "alt": "A",
      "effect": "stop_gained",
      "transcript": "ENST00000339673.11",
      "consequences": [
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.98G>A",
          "hgvs_p": "p.Trp33*",
          "transcript": "NM_004407.4",
          "protein_id": "NP_004398.1",
          "transcript_support_level": null,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 513,
          "cds_start": 98,
          "cds_end": null,
          "cds_length": 1542,
          "cdna_start": 224,
          "cdna_end": null,
          "cdna_length": 2705,
          "mane_select": "ENST00000339673.11",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.98G>A",
          "hgvs_p": "p.Trp33*",
          "transcript": "ENST00000339673.11",
          "protein_id": "ENSP00000340935.6",
          "transcript_support_level": 1,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 513,
          "cds_start": 98,
          "cds_end": null,
          "cds_length": 1542,
          "cdna_start": 224,
          "cdna_end": null,
          "cdna_length": 2705,
          "mane_select": "NM_004407.4",
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.98G>A",
          "hgvs_p": "p.Trp33*",
          "transcript": "ENST00000282479.8",
          "protein_id": "ENSP00000282479.6",
          "transcript_support_level": 1,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 497,
          "cds_start": 98,
          "cds_end": null,
          "cds_length": 1494,
          "cdna_start": 197,
          "cdna_end": null,
          "cdna_length": 2630,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.98G>A",
          "hgvs_p": "p.Trp33*",
          "transcript": "NM_001079911.3",
          "protein_id": "NP_001073380.1",
          "transcript_support_level": null,
          "aa_start": 33,
          "aa_end": null,
          "aa_length": 497,
          "cds_start": 98,
          "cds_end": null,
          "cds_length": 1494,
          "cdna_start": 224,
          "cdna_end": null,
          "cdna_length": 2657,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.185G>A",
          "hgvs_p": "p.Trp62*",
          "transcript": "XM_011531705.3",
          "protein_id": "XP_011530007.1",
          "transcript_support_level": null,
          "aa_start": 62,
          "aa_end": null,
          "aa_length": 542,
          "cds_start": 185,
          "cds_end": null,
          "cds_length": 1629,
          "cdna_start": 643,
          "cdna_end": null,
          "cdna_length": 3124,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": "W",
          "aa_alt": "*",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_gained"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "c.185G>A",
          "hgvs_p": "p.Trp62*",
          "transcript": "XM_011531706.3",
          "protein_id": "XP_011530008.1",
          "transcript_support_level": null,
          "aa_start": 62,
          "aa_end": null,
          "aa_length": 526,
          "cds_start": 185,
          "cds_end": null,
          "cds_length": 1581,
          "cdna_start": 643,
          "cdna_end": null,
          "cdna_length": 3076,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "n.98G>A",
          "hgvs_p": null,
          "transcript": "ENST00000682752.1",
          "protein_id": "ENSP00000507436.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2365,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "n.223G>A",
          "hgvs_p": null,
          "transcript": "ENST00000682781.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2660,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 7,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "n.261G>A",
          "hgvs_p": null,
          "transcript": "ENST00000683764.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2426,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "n.261G>A",
          "hgvs_p": null,
          "transcript": "ENST00000684240.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2739,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 6,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "DMP1",
          "gene_hgnc_id": 2932,
          "hgvs_c": "n.222G>A",
          "hgvs_p": null,
          "transcript": "ENST00000684389.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 2700,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.322+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000506480.5",
          "protein_id": null,
          "transcript_support_level": 3,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 821,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.356+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829286.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 457,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.348+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829287.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 699,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.347+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829288.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cds_start": -4,
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          "cdna_start": null,
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          "cdna_length": 644,
          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.301+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829289.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 584,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.356+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829290.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 645,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.369+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829291.1",
          "protein_id": null,
          "transcript_support_level": null,
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          "cdna_start": null,
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          "mane_select": null,
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          "biotype": null,
          "feature": null
        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.397+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829292.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "cdna_start": null,
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          "cdna_length": 764,
          "mane_select": null,
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          "biotype": null,
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        },
        {
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          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000249001",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.319+15915C>T",
          "hgvs_p": null,
          "transcript": "ENST00000829293.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 686,
          "mane_select": null,
          "mane_plus": null,
          "biotype": null,
          "feature": null
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "DMP1-AS1",
          "gene_hgnc_id": 58144,
          "hgvs_c": "n.366+15915C>T",
          "hgvs_p": null,
          "transcript": "NR_198971.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": -4,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": 841,
          "mane_select": null,
          "mane_plus": null,
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        {
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        },
        {
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          "consequences": [
            "downstream_gene_variant"
          ],
          "exon_rank": null,
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          "exon_count": 5,
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          "gene_symbol": "ENSG00000249001",
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          "hgvs_c": "n.*20C>T",
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          "transcript": "ENST00000829297.1",
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          "cdna_length": 799,
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      ],
      "gene_symbol": "DMP1",
      "gene_hgnc_id": 2932,
      "dbsnp": "rs766601503",
      "frequency_reference_population": 0.000012396991,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 19,
      "gnomad_exomes_af": 0.0000130388,
      "gnomad_genomes_af": 0.00000657307,
      "gnomad_exomes_ac": 18,
      "gnomad_genomes_ac": 1,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.5699999928474426,
      "computational_prediction_selected": "Pathogenic",
      "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": 0.57,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 1.028,
      "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": 8,
      "acmg_classification": "Likely_pathogenic",
      "acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
      "acmg_by_gene": [
        {
          "score": 8,
          "benign_score": 0,
          "pathogenic_score": 8,
          "criteria": [
            "PVS1_Strong",
            "PM2",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000339673.11",
          "gene_symbol": "DMP1",
          "hgnc_id": 2932,
          "effects": [
            "stop_gained"
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          "inheritance_mode": "AR",
          "hgvs_c": "c.98G>A",
          "hgvs_p": "p.Trp33*"
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        {
          "score": 8,
          "benign_score": 0,
          "pathogenic_score": 8,
          "criteria": [
            "PM2",
            "PP3_Strong",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "ENST00000506480.5",
          "gene_symbol": "ENSG00000249001",
          "hgnc_id": 58144,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.322+15915C>T",
          "hgvs_p": null
        },
        {
          "score": 8,
          "benign_score": 0,
          "pathogenic_score": 8,
          "criteria": [
            "PM2",
            "PP3_Strong",
            "PP5_Moderate"
          ],
          "verdict": "Likely_pathogenic",
          "transcript": "NR_198971.1",
          "gene_symbol": "DMP1-AS1",
          "hgnc_id": 58144,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.366+15915C>T",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "not provided",
      "clinvar_classification": "Pathogenic",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "P:1",
      "phenotype_combined": "not provided",
      "pathogenicity_classification_combined": "Pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}