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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: 6-51748375-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=51748375&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 51748375,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000371117.8",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "NM_138694.4",
"protein_id": "NP_619639.3",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
"aa_length": 4074,
"cds_start": 9241,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 9505,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "ENST00000371117.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "ENST00000371117.8",
"protein_id": "ENSP00000360158.3",
"transcript_support_level": 1,
"aa_start": 3081,
"aa_end": null,
"aa_length": 4074,
"cds_start": 9241,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 9505,
"cdna_end": null,
"cdna_length": 16271,
"mane_select": "NM_138694.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "NM_170724.3",
"protein_id": "NP_733842.2",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
"aa_length": 3396,
"cds_start": 9241,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 9505,
"cdna_end": null,
"cdna_length": 11592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "ENST00000340994.4",
"protein_id": "ENSP00000341097.4",
"transcript_support_level": 5,
"aa_start": 3081,
"aa_end": null,
"aa_length": 3396,
"cds_start": 9241,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 9502,
"cdna_end": null,
"cdna_length": 11589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_011514680.4",
"protein_id": "XP_011512982.1",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
"aa_length": 4074,
"cds_start": 9241,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 9864,
"cdna_end": null,
"cdna_length": 16630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_017010944.3",
"protein_id": "XP_016866433.1",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
"aa_length": 4074,
"cds_start": 9241,
"cds_end": null,
"cds_length": 12225,
"cdna_start": 9343,
"cdna_end": null,
"cdna_length": 16109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9166A>G",
"hgvs_p": "p.Ile3056Val",
"transcript": "XM_017010945.3",
"protein_id": "XP_016866434.1",
"transcript_support_level": null,
"aa_start": 3056,
"aa_end": null,
"aa_length": 4049,
"cds_start": 9166,
"cds_end": null,
"cds_length": 12150,
"cdna_start": 9430,
"cdna_end": null,
"cdna_length": 16196,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 57,
"exon_rank_end": null,
"exon_count": 66,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9103A>G",
"hgvs_p": "p.Ile3035Val",
"transcript": "XM_011514682.4",
"protein_id": "XP_011512984.1",
"transcript_support_level": null,
"aa_start": 3035,
"aa_end": null,
"aa_length": 4028,
"cds_start": 9103,
"cds_end": null,
"cds_length": 12087,
"cdna_start": 9367,
"cdna_end": null,
"cdna_length": 16133,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9046A>G",
"hgvs_p": "p.Ile3016Val",
"transcript": "XM_017010946.3",
"protein_id": "XP_016866435.1",
"transcript_support_level": null,
"aa_start": 3016,
"aa_end": null,
"aa_length": 4009,
"cds_start": 9046,
"cds_end": null,
"cds_length": 12030,
"cdna_start": 9310,
"cdna_end": null,
"cdna_length": 16076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 56,
"exon_rank_end": null,
"exon_count": 65,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8977A>G",
"hgvs_p": "p.Ile2993Val",
"transcript": "XM_017010947.3",
"protein_id": "XP_016866436.1",
"transcript_support_level": null,
"aa_start": 2993,
"aa_end": null,
"aa_length": 3986,
"cds_start": 8977,
"cds_end": null,
"cds_length": 11961,
"cdna_start": 9241,
"cdna_end": null,
"cdna_length": 16007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 59,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8599A>G",
"hgvs_p": "p.Ile2867Val",
"transcript": "XM_011514683.4",
"protein_id": "XP_011512985.1",
"transcript_support_level": null,
"aa_start": 2867,
"aa_end": null,
"aa_length": 3860,
"cds_start": 8599,
"cds_end": null,
"cds_length": 11583,
"cdna_start": 8863,
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"cdna_length": 15629,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8530A>G",
"hgvs_p": "p.Ile2844Val",
"transcript": "XM_011514684.4",
"protein_id": "XP_011512986.1",
"transcript_support_level": null,
"aa_start": 2844,
"aa_end": null,
"aa_length": 3837,
"cds_start": 8530,
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"cds_length": 11514,
"cdna_start": 8627,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.8530A>G",
"hgvs_p": "p.Ile2844Val",
"transcript": "XM_017010948.3",
"protein_id": "XP_016866437.1",
"transcript_support_level": null,
"aa_start": 2844,
"aa_end": null,
"aa_length": 3837,
"cds_start": 8530,
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"cdna_start": 9301,
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"mane_select": null,
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"biotype": null,
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},
{
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"canonical": false,
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"strand": false,
"consequences": [
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],
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"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
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"gene_symbol": "PKHD1",
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"hgvs_p": "p.Ile2461Val",
"transcript": "XM_017010949.3",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_011514685.2",
"protein_id": "XP_011512987.1",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
"aa_length": 3416,
"cds_start": 9241,
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"cdna_start": 9505,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_017010950.2",
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_011514686.3",
"protein_id": "XP_011512988.1",
"transcript_support_level": null,
"aa_start": 3081,
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"aa_length": 3402,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 58,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val",
"transcript": "XM_011514687.2",
"protein_id": "XP_011512989.1",
"transcript_support_level": null,
"aa_start": 3081,
"aa_end": null,
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"cds_start": 9241,
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"feature": null
},
{
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"strand": false,
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],
"exon_rank": 58,
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"exon_count": 59,
"intron_rank": null,
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"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.9241A>G",
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"transcript": "XM_011514688.3",
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},
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.3316A>G",
"hgvs_p": "p.Ile1106Val",
"transcript": "XM_011514690.4",
"protein_id": "XP_011512992.1",
"transcript_support_level": null,
"aa_start": 1106,
"aa_end": null,
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"cds_start": 3316,
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"cdna_start": 3403,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "c.3316A>G",
"hgvs_p": "p.Ile1106Val",
"transcript": "XM_011514691.4",
"protein_id": "XP_011512993.1",
"transcript_support_level": null,
"aa_start": 1106,
"aa_end": null,
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"cds_start": 3316,
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"cds_length": 6300,
"cdna_start": 9425,
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"cdna_length": 16191,
"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": 58,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"hgvs_c": "n.9505A>G",
"hgvs_p": null,
"transcript": "XR_001743469.2",
"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": 11764,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PKHD1",
"gene_hgnc_id": 9016,
"dbsnp": "rs142146981",
"frequency_reference_population": 0.0002509421,
"hom_count_reference_population": 2,
"allele_count_reference_population": 405,
"gnomad_exomes_af": 0.000262692,
"gnomad_genomes_af": 0.000138038,
"gnomad_exomes_ac": 384,
"gnomad_genomes_ac": 21,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7327884435653687,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.605,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1729,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.746,
"phylop100way_prediction": "Uncertain_significance",
"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": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000371117.8",
"gene_symbol": "PKHD1",
"hgnc_id": 9016,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.9241A>G",
"hgvs_p": "p.Ile3081Val"
}
],
"clinvar_disease": "Autosomal recessive polycystic kidney disease,Polycystic kidney disease 4,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:8",
"phenotype_combined": "not provided|Autosomal recessive polycystic kidney disease|not specified|Polycystic kidney disease 4",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}