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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: 3-38141150-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38141150&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "3",
      "pos": 38141150,
      "ref": "T",
      "alt": "C",
      "effect": "stop_lost",
      "transcript": "NM_001365876.1",
      "consequences": [
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.755T>C",
          "hgvs_p": "p.Leu252Pro",
          "transcript": "NM_002468.5",
          "protein_id": "NP_002459.3",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 296,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 891,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000650905.2",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_002468.5"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.755T>C",
          "hgvs_p": "p.Leu252Pro",
          "transcript": "ENST00000650905.2",
          "protein_id": "ENSP00000498360.2",
          "transcript_support_level": null,
          "aa_start": 252,
          "aa_end": null,
          "aa_length": 296,
          "cds_start": 755,
          "cds_end": null,
          "cds_length": 891,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_002468.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000650905.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.779T>C",
          "hgvs_p": "p.Leu260Pro",
          "transcript": "ENST00000421516.3",
          "protein_id": "ENSP00000391753.3",
          "transcript_support_level": 1,
          "aa_start": 260,
          "aa_end": null,
          "aa_length": 304,
          "cds_start": 779,
          "cds_end": null,
          "cds_length": 915,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000421516.3"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.620T>C",
          "hgvs_p": "p.Leu207Pro",
          "transcript": "ENST00000417037.8",
          "protein_id": "ENSP00000401399.4",
          "transcript_support_level": 1,
          "aa_start": 207,
          "aa_end": null,
          "aa_length": 251,
          "cds_start": 620,
          "cds_end": null,
          "cds_length": 756,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000417037.8"
        },
        {
          "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": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "n.858T>C",
          "hgvs_p": null,
          "transcript": "ENST00000416282.3",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000416282.3"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.736T>C",
          "hgvs_p": "p.Ter246Argext*?",
          "transcript": "NM_001365876.1",
          "protein_id": "NP_001352805.1",
          "transcript_support_level": null,
          "aa_start": 246,
          "aa_end": null,
          "aa_length": 245,
          "cds_start": 736,
          "cds_end": null,
          "cds_length": 738,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001365876.1"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.736T>C",
          "hgvs_p": "p.Ter246Argext*?",
          "transcript": "ENST00000652213.1",
          "protein_id": "ENSP00000498576.1",
          "transcript_support_level": null,
          "aa_start": 246,
          "aa_end": null,
          "aa_length": 245,
          "cds_start": 736,
          "cds_end": null,
          "cds_length": 738,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000652213.1"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.712T>C",
          "hgvs_p": "p.Ter238Argext*?",
          "transcript": "NM_001374787.1",
          "protein_id": "NP_001361716.1",
          "transcript_support_level": null,
          "aa_start": 238,
          "aa_end": null,
          "aa_length": 237,
          "cds_start": 712,
          "cds_end": null,
          "cds_length": 714,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001374787.1"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.601T>C",
          "hgvs_p": "p.Ter201Argext*?",
          "transcript": "NM_001365877.1",
          "protein_id": "NP_001352806.1",
          "transcript_support_level": null,
          "aa_start": 201,
          "aa_end": null,
          "aa_length": 200,
          "cds_start": 601,
          "cds_end": null,
          "cds_length": 603,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001365877.1"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.574T>C",
          "hgvs_p": "p.Ter192Argext*?",
          "transcript": "NM_001172569.3",
          "protein_id": "NP_001166040.2",
          "transcript_support_level": null,
          "aa_start": 192,
          "aa_end": null,
          "aa_length": 191,
          "cds_start": 574,
          "cds_end": null,
          "cds_length": 576,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001172569.3"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.574T>C",
          "hgvs_p": "p.Ter192Argext*?",
          "transcript": "ENST00000651800.2",
          "protein_id": "ENSP00000499012.2",
          "transcript_support_level": null,
          "aa_start": 192,
          "aa_end": null,
          "aa_length": 191,
          "cds_start": 574,
          "cds_end": null,
          "cds_length": 576,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000651800.2"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.535T>C",
          "hgvs_p": "p.Ter179Argext*?",
          "transcript": "ENST00000699086.1",
          "protein_id": "ENSP00000514121.1",
          "transcript_support_level": null,
          "aa_start": 179,
          "aa_end": null,
          "aa_length": 178,
          "cds_start": 535,
          "cds_end": null,
          "cds_length": 537,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000699086.1"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.439T>C",
          "hgvs_p": "p.Ter147Argext*?",
          "transcript": "NM_001172566.2",
          "protein_id": "NP_001166037.2",
          "transcript_support_level": null,
          "aa_start": 147,
          "aa_end": null,
          "aa_length": 146,
          "cds_start": 439,
          "cds_end": null,
          "cds_length": 441,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001172566.2"
        },
        {
          "aa_ref": "*",
          "aa_alt": "R",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "stop_lost"
          ],
          "exon_rank": 3,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.439T>C",
          "hgvs_p": "p.Ter147Argext*?",
          "transcript": "ENST00000650112.2",
          "protein_id": "ENSP00000497991.2",
          "transcript_support_level": null,
          "aa_start": 147,
          "aa_end": null,
          "aa_length": 146,
          "cds_start": 439,
          "cds_end": null,
          "cds_length": 441,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000650112.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.791T>C",
          "hgvs_p": "p.Leu264Pro",
          "transcript": "ENST00000969068.1",
          "protein_id": "ENSP00000639127.1",
          "transcript_support_level": null,
          "aa_start": 264,
          "aa_end": null,
          "aa_length": 308,
          "cds_start": 791,
          "cds_end": null,
          "cds_length": 927,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000969068.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.779T>C",
          "hgvs_p": "p.Leu260Pro",
          "transcript": "NM_001172567.2",
          "protein_id": "NP_001166038.2",
          "transcript_support_level": null,
          "aa_start": 260,
          "aa_end": null,
          "aa_length": 304,
          "cds_start": 779,
          "cds_end": null,
          "cds_length": 915,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001172567.2"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 5,
          "exon_rank_end": null,
          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.758T>C",
          "hgvs_p": "p.Leu253Pro",
          "transcript": "ENST00000969067.1",
          "protein_id": "ENSP00000639126.1",
          "transcript_support_level": null,
          "aa_start": 253,
          "aa_end": null,
          "aa_length": 297,
          "cds_start": 758,
          "cds_end": null,
          "cds_length": 894,
          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.725T>C",
          "hgvs_p": "p.Leu242Pro",
          "transcript": "ENST00000862995.1",
          "protein_id": "ENSP00000533054.1",
          "transcript_support_level": null,
          "aa_start": 242,
          "aa_end": null,
          "aa_length": 286,
          "cds_start": 725,
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          "cds_length": 861,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000862995.1"
        },
        {
          "aa_ref": "L",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 5,
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          "exon_count": 5,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.683T>C",
          "hgvs_p": "p.Leu228Pro",
          "transcript": "ENST00000969069.1",
          "protein_id": "ENSP00000639128.1",
          "transcript_support_level": null,
          "aa_start": 228,
          "aa_end": null,
          "aa_length": 272,
          "cds_start": 683,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000969069.1"
        },
        {
          "aa_ref": "L",
          "aa_alt": "P",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 4,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "c.644T>C",
          "hgvs_p": "p.Leu215Pro",
          "transcript": "ENST00000969070.1",
          "protein_id": "ENSP00000639129.1",
          "transcript_support_level": null,
          "aa_start": 215,
          "aa_end": null,
          "aa_length": 259,
          "cds_start": 644,
          "cds_end": null,
          "cds_length": 780,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000969070.1"
        },
        {
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        {
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          "gene_symbol": "MYD88",
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          "gene_symbol": "MYD88",
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          "hgvs_c": "n.983T>C",
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          "transcript": "ENST00000652590.1",
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          "biotype": "retained_intron",
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        {
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          "protein_coding": false,
          "strand": true,
          "consequences": [
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          "exon_count": 3,
          "intron_rank": null,
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          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "n.1844T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699084.1",
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          "transcript_support_level": null,
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          "cdna_start": null,
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          "biotype": "retained_intron",
          "feature": "ENST00000699084.1"
        },
        {
          "aa_ref": null,
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          "protein_coding": false,
          "strand": true,
          "consequences": [
            "non_coding_transcript_exon_variant"
          ],
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          "exon_count": 4,
          "intron_rank": null,
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          "gene_symbol": "MYD88",
          "gene_hgnc_id": 7562,
          "hgvs_c": "n.1620T>C",
          "hgvs_p": null,
          "transcript": "ENST00000699085.1",
          "protein_id": null,
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          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000699085.1"
        }
      ],
      "gene_symbol": "MYD88",
      "gene_hgnc_id": 7562,
      "dbsnp": "rs387907272",
      "frequency_reference_population": 0.000026021338,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 42,
      "gnomad_exomes_af": 0.0000266803,
      "gnomad_genomes_af": 0.0000196967,
      "gnomad_exomes_ac": 39,
      "gnomad_genomes_ac": 3,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": 0,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.7411302328109741,
      "computational_prediction_selected": "Uncertain_significance",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.735,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9974,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.13,
      "bayesdelnoaf_prediction": "Uncertain_significance",
      "phylop100way_score": 7.865,
      "phylop100way_prediction": "Pathogenic",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": 4,
      "acmg_classification": "Uncertain_significance",
      "acmg_criteria": "PM2,PM4",
      "acmg_by_gene": [
        {
          "score": 4,
          "benign_score": 0,
          "pathogenic_score": 4,
          "criteria": [
            "PM2",
            "PM4"
          ],
          "verdict": "Uncertain_significance",
          "transcript": "NM_001365876.1",
          "gene_symbol": "MYD88",
          "hgnc_id": 7562,
          "effects": [
            "stop_lost"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.736T>C",
          "hgvs_p": "p.Ter246Argext*?"
        }
      ],
      "clinvar_disease": " Waldenstrom, diffuse, large B-cell, somatic,Macroglobulinemia,Malignant lymphoma,Neoplasm,Pyogenic bacterial infections due to MyD88 deficiency",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "criteria provided, single submitter",
      "clinvar_submissions_summary": "US:2",
      "phenotype_combined": "Macroglobulinemia, Waldenstrom, somatic|Pyogenic bacterial infections due to MyD88 deficiency|Malignant lymphoma, large B-cell, diffuse|Neoplasm",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}