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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: 1-116395224-T-C (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=116395224&ref=T&alt=C&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "1",
      "pos": 116395224,
      "ref": "T",
      "alt": "C",
      "effect": "missense_variant",
      "transcript": "NM_000701.8",
      "consequences": [
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "NM_000701.8",
          "protein_id": "NP_000692.2",
          "transcript_support_level": null,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000295598.10",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_000701.8"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": true,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "ENST00000295598.10",
          "protein_id": "ENSP00000295598.5",
          "transcript_support_level": 1,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_000701.8",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000295598.10"
        },
        {
          "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": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.411-2198A>G",
          "hgvs_p": null,
          "transcript": "ENST00000608511.6",
          "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": "pseudogene",
          "feature": "ENST00000608511.6"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1934T>C",
          "hgvs_p": "p.Ile645Thr",
          "transcript": "ENST00000897942.1",
          "protein_id": "ENSP00000568001.1",
          "transcript_support_level": null,
          "aa_start": 645,
          "aa_end": null,
          "aa_length": 1076,
          "cds_start": 1934,
          "cds_end": null,
          "cds_length": 3231,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897942.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1814T>C",
          "hgvs_p": "p.Ile605Thr",
          "transcript": "ENST00000945201.1",
          "protein_id": "ENSP00000615260.1",
          "transcript_support_level": null,
          "aa_start": 605,
          "aa_end": null,
          "aa_length": 1036,
          "cds_start": 1814,
          "cds_end": null,
          "cds_length": 3111,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000945201.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "NM_001160233.2",
          "protein_id": "NP_001153705.1",
          "transcript_support_level": null,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001160233.2"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "ENST00000537345.5",
          "protein_id": "ENSP00000445306.1",
          "transcript_support_level": 2,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000537345.5"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 14,
          "exon_rank_end": null,
          "exon_count": 24,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "ENST00000897938.1",
          "protein_id": "ENSP00000567997.1",
          "transcript_support_level": null,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1023,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3072,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897938.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1772T>C",
          "hgvs_p": "p.Ile591Thr",
          "transcript": "ENST00000897941.1",
          "protein_id": "ENSP00000568000.1",
          "transcript_support_level": null,
          "aa_start": 591,
          "aa_end": null,
          "aa_length": 1022,
          "cds_start": 1772,
          "cds_end": null,
          "cds_length": 3069,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897941.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "ENST00000897939.1",
          "protein_id": "ENSP00000567998.1",
          "transcript_support_level": null,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1019,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3060,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897939.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr",
          "transcript": "ENST00000897944.1",
          "protein_id": "ENSP00000568003.1",
          "transcript_support_level": null,
          "aa_start": 592,
          "aa_end": null,
          "aa_length": 1019,
          "cds_start": 1775,
          "cds_end": null,
          "cds_length": 3060,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000897944.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1682T>C",
          "hgvs_p": "p.Ile561Thr",
          "transcript": "NM_001160234.2",
          "protein_id": "NP_001153706.1",
          "transcript_support_level": null,
          "aa_start": 561,
          "aa_end": null,
          "aa_length": 992,
          "cds_start": 1682,
          "cds_end": null,
          "cds_length": 2979,
          "cdna_start": null,
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          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "I",
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 13,
          "exon_rank_end": null,
          "exon_count": 23,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1682T>C",
          "hgvs_p": "p.Ile561Thr",
          "transcript": "ENST00000369496.8",
          "protein_id": "ENSP00000358508.4",
          "transcript_support_level": 2,
          "aa_start": 561,
          "aa_end": null,
          "aa_length": 992,
          "cds_start": 1682,
          "cds_end": null,
          "cds_length": 2979,
          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000369496.8"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
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          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1661T>C",
          "hgvs_p": "p.Ile554Thr",
          "transcript": "ENST00000897943.1",
          "protein_id": "ENSP00000568002.1",
          "transcript_support_level": null,
          "aa_start": 554,
          "aa_end": null,
          "aa_length": 985,
          "cds_start": 1661,
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          "biotype": "protein_coding",
          "feature": "ENST00000897943.1"
        },
        {
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          "canonical": false,
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          "strand": true,
          "consequences": [
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          ],
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          "exon_count": 22,
          "intron_rank": null,
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          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1640T>C",
          "hgvs_p": "p.Ile547Thr",
          "transcript": "ENST00000945199.1",
          "protein_id": "ENSP00000615258.1",
          "transcript_support_level": null,
          "aa_start": 547,
          "aa_end": null,
          "aa_length": 978,
          "cds_start": 1640,
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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": "ENST00000945199.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 12,
          "exon_rank_end": null,
          "exon_count": 22,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1571T>C",
          "hgvs_p": "p.Ile524Thr",
          "transcript": "ENST00000945200.1",
          "protein_id": "ENSP00000615259.1",
          "transcript_support_level": null,
          "aa_start": 524,
          "aa_end": null,
          "aa_length": 955,
          "cds_start": 1571,
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          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000945200.1"
        },
        {
          "aa_ref": "I",
          "aa_alt": "T",
          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "missense_variant"
          ],
          "exon_rank": 11,
          "exon_rank_end": null,
          "exon_count": 21,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.1307T>C",
          "hgvs_p": "p.Ile436Thr",
          "transcript": "ENST00000897940.1",
          "protein_id": "ENSP00000567999.1",
          "transcript_support_level": null,
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          "aa_end": null,
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          "biotype": "protein_coding",
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        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": true,
          "consequences": [
            "intron_variant"
          ],
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          "exon_count": 13,
          "intron_rank": 3,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1",
          "gene_hgnc_id": 799,
          "hgvs_c": "c.184-1374T>C",
          "hgvs_p": null,
          "transcript": "ENST00000897945.1",
          "protein_id": "ENSP00000568004.1",
          "transcript_support_level": null,
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          "cds_start": null,
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          "biotype": "protein_coding",
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        },
        {
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          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.657-2198A>G",
          "hgvs_p": null,
          "transcript": "ENST00000674941.1",
          "protein_id": null,
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          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "ENST00000674941.1"
        },
        {
          "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": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.184-2198A>G",
          "hgvs_p": null,
          "transcript": "ENST00000675524.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
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          "cds_length": null,
          "cdna_start": null,
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          "cdna_length": null,
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          "feature": "ENST00000675524.1"
        },
        {
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          "exon_count": 4,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.385+5672A>G",
          "hgvs_p": null,
          "transcript": "ENST00000675607.1",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": null,
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          "cds_length": null,
          "cdna_start": null,
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          "biotype": "pseudogene",
          "feature": "ENST00000675607.1"
        },
        {
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          "protein_coding": false,
          "strand": false,
          "consequences": [
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          "exon_count": 4,
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          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.889-2198A>G",
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          "transcript": "ENST00000675742.1",
          "protein_id": null,
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          "cdna_start": null,
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          "cdna_length": null,
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          "biotype": "pseudogene",
          "feature": "ENST00000675742.1"
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        {
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          "exon_count": 3,
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          "gene_symbol": "ATP1A1-AS1",
          "gene_hgnc_id": 28262,
          "hgvs_c": "n.401-2198A>G",
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          "transcript": "NR_027646.1",
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          "cds_length": null,
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          "biotype": "pseudogene",
          "feature": "NR_027646.1"
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      ],
      "gene_symbol": "ATP1A1",
      "gene_hgnc_id": 799,
      "dbsnp": "rs1553192086",
      "frequency_reference_population": 0.000001368107,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 2,
      "gnomad_exomes_af": 0.00000136811,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 2,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": 0.8715988397598267,
      "computational_prediction_selected": "Pathogenic",
      "computational_source_selected": "MetaRNN",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": 0.863,
      "revel_prediction": "Pathogenic",
      "alphamissense_score": 0.9199,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": 0.29,
      "bayesdelnoaf_prediction": "Pathogenic",
      "phylop100way_score": 8.011,
      "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": 18,
      "acmg_classification": "Pathogenic",
      "acmg_criteria": "PS3,PM1,PM2,PP3_Moderate,PP5_Very_Strong",
      "acmg_by_gene": [
        {
          "score": 18,
          "benign_score": 0,
          "pathogenic_score": 18,
          "criteria": [
            "PS3",
            "PM1",
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "NM_000701.8",
          "gene_symbol": "ATP1A1",
          "hgnc_id": 799,
          "effects": [
            "missense_variant"
          ],
          "inheritance_mode": "AD",
          "hgvs_c": "c.1775T>C",
          "hgvs_p": "p.Ile592Thr"
        },
        {
          "score": 16,
          "benign_score": 0,
          "pathogenic_score": 16,
          "criteria": [
            "PS3",
            "PM2",
            "PP3_Moderate",
            "PP5_Very_Strong"
          ],
          "verdict": "Pathogenic",
          "transcript": "ENST00000608511.6",
          "gene_symbol": "ATP1A1-AS1",
          "hgnc_id": 28262,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.411-2198A>G",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": " axonal, type 2DD,Charcot-Marie-Tooth disease type 2A2,Charcot-Marie-tooth disease,not provided",
      "clinvar_classification": "Pathogenic/Likely pathogenic",
      "clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
      "clinvar_submissions_summary": "P:1 LP:1",
      "phenotype_combined": "Charcot-Marie-tooth disease, axonal, type 2DD|not provided|Charcot-Marie-Tooth disease type 2A2",
      "pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
      "custom_annotations": null
    }
  ],
  "message": null
}
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