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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: 10-3138248-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=3138248&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 3138248,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000224949.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.3007G>A",
"hgvs_p": "p.Ala1003Thr",
"transcript": "NM_014889.4",
"protein_id": "NP_055704.2",
"transcript_support_level": null,
"aa_start": 1003,
"aa_end": null,
"aa_length": 1037,
"cds_start": 3007,
"cds_end": null,
"cds_length": 3114,
"cdna_start": 3017,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": "ENST00000224949.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.3007G>A",
"hgvs_p": "p.Ala1003Thr",
"transcript": "ENST00000224949.9",
"protein_id": "ENSP00000224949.4",
"transcript_support_level": 1,
"aa_start": 1003,
"aa_end": null,
"aa_length": 1037,
"cds_start": 3007,
"cds_end": null,
"cds_length": 3114,
"cdna_start": 3017,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": "NM_014889.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.3010G>A",
"hgvs_p": "p.Ala1004Thr",
"transcript": "ENST00000380989.6",
"protein_id": "ENSP00000370377.2",
"transcript_support_level": 1,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1038,
"cds_start": 3010,
"cds_end": null,
"cds_length": 3117,
"cdna_start": 3079,
"cdna_end": null,
"cdna_length": 3487,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "n.2830G>A",
"hgvs_p": null,
"transcript": "ENST00000464395.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 3240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.3010G>A",
"hgvs_p": "p.Ala1004Thr",
"transcript": "NM_001242307.2",
"protein_id": "NP_001229236.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1038,
"cds_start": 3010,
"cds_end": null,
"cds_length": 3117,
"cdna_start": 3020,
"cdna_end": null,
"cdna_length": 3430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Ala995Thr",
"transcript": "NM_001347729.1",
"protein_id": "NP_001334658.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1029,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3090,
"cdna_start": 3486,
"cdna_end": null,
"cdna_length": 3897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2959G>A",
"hgvs_p": "p.Ala987Thr",
"transcript": "ENST00000678987.1",
"protein_id": "ENSP00000504462.1",
"transcript_support_level": null,
"aa_start": 987,
"aa_end": null,
"aa_length": 1021,
"cds_start": 2959,
"cds_end": null,
"cds_length": 3066,
"cdna_start": 2976,
"cdna_end": null,
"cdna_length": 3374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2884G>A",
"hgvs_p": "p.Ala962Thr",
"transcript": "ENST00000678441.1",
"protein_id": "ENSP00000504785.1",
"transcript_support_level": null,
"aa_start": 962,
"aa_end": null,
"aa_length": 996,
"cds_start": 2884,
"cds_end": null,
"cds_length": 2991,
"cdna_start": 2902,
"cdna_end": null,
"cdna_length": 3294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2881G>A",
"hgvs_p": "p.Ala961Thr",
"transcript": "ENST00000678370.1",
"protein_id": "ENSP00000504540.1",
"transcript_support_level": null,
"aa_start": 961,
"aa_end": null,
"aa_length": 995,
"cds_start": 2881,
"cds_end": null,
"cds_length": 2988,
"cdna_start": 2915,
"cdna_end": null,
"cdna_length": 3307,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2872G>A",
"hgvs_p": "p.Ala958Thr",
"transcript": "ENST00000676953.1",
"protein_id": "ENSP00000504468.1",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 992,
"cds_start": 2872,
"cds_end": null,
"cds_length": 2979,
"cdna_start": 2879,
"cdna_end": null,
"cdna_length": 3277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2809G>A",
"hgvs_p": "p.Ala937Thr",
"transcript": "NM_001347725.2",
"protein_id": "NP_001334654.1",
"transcript_support_level": null,
"aa_start": 937,
"aa_end": null,
"aa_length": 971,
"cds_start": 2809,
"cds_end": null,
"cds_length": 2916,
"cdna_start": 2819,
"cdna_end": null,
"cdna_length": 3229,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2809G>A",
"hgvs_p": "p.Ala937Thr",
"transcript": "ENST00000678436.1",
"protein_id": "ENSP00000503187.1",
"transcript_support_level": null,
"aa_start": 937,
"aa_end": null,
"aa_length": 971,
"cds_start": 2809,
"cds_end": null,
"cds_length": 2916,
"cdna_start": 2844,
"cdna_end": null,
"cdna_length": 3242,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2785G>A",
"hgvs_p": "p.Ala929Thr",
"transcript": "NM_001347730.1",
"protein_id": "NP_001334659.1",
"transcript_support_level": null,
"aa_start": 929,
"aa_end": null,
"aa_length": 963,
"cds_start": 2785,
"cds_end": null,
"cds_length": 2892,
"cdna_start": 3288,
"cdna_end": null,
"cdna_length": 3699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2713G>A",
"hgvs_p": "p.Ala905Thr",
"transcript": "NM_001242309.1",
"protein_id": "NP_001229238.1",
"transcript_support_level": null,
"aa_start": 905,
"aa_end": null,
"aa_length": 939,
"cds_start": 2713,
"cds_end": null,
"cds_length": 2820,
"cdna_start": 2775,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2713G>A",
"hgvs_p": "p.Ala905Thr",
"transcript": "ENST00000451104.6",
"protein_id": "ENSP00000401201.2",
"transcript_support_level": 2,
"aa_start": 905,
"aa_end": null,
"aa_length": 939,
"cds_start": 2713,
"cds_end": null,
"cds_length": 2820,
"cdna_start": 2775,
"cdna_end": null,
"cdna_length": 3183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Ala798Thr",
"transcript": "NM_001347727.2",
"protein_id": "NP_001334656.1",
"transcript_support_level": null,
"aa_start": 798,
"aa_end": null,
"aa_length": 832,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2499,
"cdna_start": 2973,
"cdna_end": null,
"cdna_length": 3383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2392G>A",
"hgvs_p": "p.Ala798Thr",
"transcript": "ENST00000380994.6",
"protein_id": "ENSP00000370382.2",
"transcript_support_level": 5,
"aa_start": 798,
"aa_end": null,
"aa_length": 832,
"cds_start": 2392,
"cds_end": null,
"cds_length": 2499,
"cdna_start": 2875,
"cdna_end": null,
"cdna_length": 3274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.2194G>A",
"hgvs_p": "p.Ala732Thr",
"transcript": "NM_001347726.2",
"protein_id": "NP_001334655.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 766,
"cds_start": 2194,
"cds_end": null,
"cds_length": 2301,
"cdna_start": 2775,
"cdna_end": null,
"cdna_length": 3185,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Ala568Thr",
"transcript": "NM_001347728.2",
"protein_id": "NP_001334657.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 602,
"cds_start": 1702,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 3012,
"cdna_end": null,
"cdna_length": 3422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "c.1351G>A",
"hgvs_p": "p.Ala451Thr",
"transcript": "ENST00000678811.1",
"protein_id": "ENSP00000504078.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 485,
"cds_start": 1351,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1352,
"cdna_end": null,
"cdna_length": 1762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "n.423G>A",
"hgvs_p": null,
"transcript": "ENST00000490510.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PITRM1",
"gene_hgnc_id": 17663,
"hgvs_c": "n.2994G>A",
"hgvs_p": null,
"transcript": "ENST00000676519.1",
"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": 3392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
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},
{
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},
{
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},
{
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"consequences": [
"intron_variant"
],
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}
],
"gene_symbol": "PITRM1",
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"dbsnp": "rs1488536802",
"frequency_reference_population": 0.000032234668,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.0000301171,
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"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12808221578598022,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.009,
"revel_prediction": "Benign",
"alphamissense_score": 0.0723,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.175,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000224949.9",
"gene_symbol": "PITRM1",
"hgnc_id": 17663,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3007G>A",
"hgvs_p": "p.Ala1003Thr"
},
{
"score": 0,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000441377.2",
"gene_symbol": "ENSG00000278419",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.120+2410C>T",
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}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}