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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: 5-78039267-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=78039267&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 78039267,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003664.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "NM_003664.5",
"protein_id": "NP_003655.3",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000255194.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003664.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000255194.11",
"protein_id": "ENSP00000255194.7",
"transcript_support_level": 1,
"aa_start": 862,
"aa_end": null,
"aa_length": 1094,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003664.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000255194.11"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2438C>T",
"hgvs_p": "p.Thr813Ile",
"transcript": "ENST00000519295.7",
"protein_id": "ENSP00000430597.1",
"transcript_support_level": 1,
"aa_start": 813,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2438,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000519295.7"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000913629.1",
"protein_id": "ENSP00000583688.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1093,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913629.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2579C>T",
"hgvs_p": "p.Thr860Ile",
"transcript": "ENST00000909857.1",
"protein_id": "ENSP00000579916.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 1092,
"cds_start": 2579,
"cds_end": null,
"cds_length": 3279,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909857.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2576C>T",
"hgvs_p": "p.Thr859Ile",
"transcript": "ENST00000913630.1",
"protein_id": "ENSP00000583689.1",
"transcript_support_level": null,
"aa_start": 859,
"aa_end": null,
"aa_length": 1091,
"cds_start": 2576,
"cds_end": null,
"cds_length": 3276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913630.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000695515.1",
"protein_id": "ENSP00000511978.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695515.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000695511.1",
"protein_id": "ENSP00000511974.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1053,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695511.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000959993.1",
"protein_id": "ENSP00000630052.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1053,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959993.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2579C>T",
"hgvs_p": "p.Thr860Ile",
"transcript": "ENST00000695454.1",
"protein_id": "ENSP00000511922.1",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2579,
"cds_end": null,
"cds_length": 3156,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695454.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2450C>T",
"hgvs_p": "p.Thr817Ile",
"transcript": "ENST00000695513.1",
"protein_id": "ENSP00000511976.1",
"transcript_support_level": null,
"aa_start": 817,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2450,
"cds_end": null,
"cds_length": 3150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695513.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2438C>T",
"hgvs_p": "p.Thr813Ile",
"transcript": "NM_001271769.2",
"protein_id": "NP_001258698.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2438,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271769.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2408C>T",
"hgvs_p": "p.Thr803Ile",
"transcript": "ENST00000909858.1",
"protein_id": "ENSP00000579917.1",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 1035,
"cds_start": 2408,
"cds_end": null,
"cds_length": 3108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909858.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2528C>T",
"hgvs_p": "p.Thr843Ile",
"transcript": "ENST00000695453.1",
"protein_id": "ENSP00000511921.1",
"transcript_support_level": null,
"aa_start": 843,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2528,
"cds_end": null,
"cds_length": 3105,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695453.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2405C>T",
"hgvs_p": "p.Thr802Ile",
"transcript": "ENST00000695512.1",
"protein_id": "ENSP00000511975.1",
"transcript_support_level": null,
"aa_start": 802,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2405,
"cds_end": null,
"cds_length": 3105,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695512.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile",
"transcript": "ENST00000695510.1",
"protein_id": "ENSP00000511973.1",
"transcript_support_level": null,
"aa_start": 862,
"aa_end": null,
"aa_length": 1008,
"cds_start": 2585,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695510.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2438C>T",
"hgvs_p": "p.Thr813Ile",
"transcript": "ENST00000695455.1",
"protein_id": "ENSP00000511923.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2438,
"cds_end": null,
"cds_length": 3015,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695455.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.2261C>T",
"hgvs_p": "p.Thr754Ile",
"transcript": "ENST00000913631.1",
"protein_id": "ENSP00000583690.1",
"transcript_support_level": null,
"aa_start": 754,
"aa_end": null,
"aa_length": 986,
"cds_start": 2261,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913631.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "c.1784C>T",
"hgvs_p": "p.Thr595Ile",
"transcript": "ENST00000695450.1",
"protein_id": "ENSP00000511919.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 827,
"cds_start": 1784,
"cds_end": null,
"cds_length": 2484,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000695450.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.385C>T",
"hgvs_p": null,
"transcript": "ENST00000523204.2",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000523204.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.2478C>T",
"hgvs_p": null,
"transcript": "ENST00000695447.1",
"protein_id": "ENSP00000511917.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000695447.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"hgvs_c": "n.*2347C>T",
"hgvs_p": null,
"transcript": "ENST00000695451.1",
"protein_id": "ENSP00000511920.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
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{
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"biotype": "retained_intron",
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"exon_count": 8,
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{
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{
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{
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"upstream_gene_variant"
],
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"gene_symbol": "AP3B1",
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"transcript": "ENST00000522901.1",
"protein_id": "ENSP00000429228.1",
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"biotype": "protein_coding",
"feature": "ENST00000522901.1"
}
],
"gene_symbol": "AP3B1",
"gene_hgnc_id": 566,
"dbsnp": "rs146624866",
"frequency_reference_population": 0.0009179066,
"hom_count_reference_population": 12,
"allele_count_reference_population": 1481,
"gnomad_exomes_af": 0.000527646,
"gnomad_genomes_af": 0.00466351,
"gnomad_exomes_ac": 771,
"gnomad_genomes_ac": 710,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009931504726409912,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.185,
"revel_prediction": "Benign",
"alphamissense_score": 0.0915,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.954,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003664.5",
"gene_symbol": "AP3B1",
"hgnc_id": 566,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2585C>T",
"hgvs_p": "p.Thr862Ile"
}
],
"clinvar_disease": "AP3B1-related disorder,Autoinflammatory syndrome,Hermansky-Pudlak syndrome 2,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:3",
"phenotype_combined": "not specified|Hermansky-Pudlak syndrome 2|AP3B1-related disorder|Autoinflammatory syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}