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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: 16-29813541-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=29813541&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 29813541,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000358758.12",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_145239.3",
"protein_id": "NP_660282.2",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 683,
"cdna_end": null,
"cdna_length": 2462,
"mane_select": "ENST00000358758.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000358758.12",
"protein_id": "ENSP00000351608.7",
"transcript_support_level": 1,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 683,
"cdna_end": null,
"cdna_length": 2462,
"mane_select": "NM_145239.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"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": "ENSG00000280893",
"gene_hgnc_id": null,
"hgvs_c": "n.487C>T",
"hgvs_p": null,
"transcript": "ENST00000609618.2",
"protein_id": "ENSP00000476774.2",
"transcript_support_level": 5,
"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": 2252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_001256442.2",
"protein_id": "NP_001243371.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 394,
"cds_start": 487,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 683,
"cdna_end": null,
"cdna_length": 2624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_001438121.1",
"protein_id": "NP_001425050.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 394,
"cds_start": 487,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 711,
"cdna_end": null,
"cdna_length": 2652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000567659.3",
"protein_id": "ENSP00000456226.1",
"transcript_support_level": 2,
"aa_start": 163,
"aa_end": null,
"aa_length": 394,
"cds_start": 487,
"cds_end": null,
"cds_length": 1185,
"cdna_start": 685,
"cdna_end": null,
"cdna_length": 1470,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_001438120.1",
"protein_id": "NP_001425049.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 711,
"cdna_end": null,
"cdna_length": 2490,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000572820.2",
"protein_id": "ENSP00000458291.2",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 613,
"cdna_end": null,
"cdna_length": 2403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000637064.1",
"protein_id": "ENSP00000490826.1",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 612,
"cdna_end": null,
"cdna_length": 2153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_001256443.2",
"protein_id": "NP_001243372.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 299,
"cds_start": 487,
"cds_end": null,
"cds_length": 900,
"cdna_start": 711,
"cdna_end": null,
"cdna_length": 3051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "NM_001438122.1",
"protein_id": "NP_001425051.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 299,
"cds_start": 487,
"cds_end": null,
"cds_length": 900,
"cdna_start": 683,
"cdna_end": null,
"cdna_length": 3023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000300797.7",
"protein_id": "ENSP00000300797.6",
"transcript_support_level": 2,
"aa_start": 163,
"aa_end": null,
"aa_length": 299,
"cds_start": 487,
"cds_end": null,
"cds_length": 900,
"cdna_start": 663,
"cdna_end": null,
"cdna_length": 3002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000647876.1",
"protein_id": "ENSP00000498021.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 299,
"cds_start": 487,
"cds_end": null,
"cds_length": 900,
"cdna_start": 726,
"cdna_end": null,
"cdna_length": 2867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000636619.1",
"protein_id": "ENSP00000489669.1",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 287,
"cds_start": 487,
"cds_end": null,
"cds_length": 864,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 2065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "ENST00000637403.1",
"protein_id": "ENSP00000489782.1",
"transcript_support_level": 5,
"aa_start": 163,
"aa_end": null,
"aa_length": 286,
"cds_start": 487,
"cds_end": null,
"cds_length": 861,
"cdna_start": 614,
"cdna_end": null,
"cdna_length": 2033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "XM_017022887.3",
"protein_id": "XP_016878376.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 346,
"cds_start": 487,
"cds_end": null,
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"cdna_start": 683,
"cdna_end": null,
"cdna_length": 1254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*",
"transcript": "XM_017022889.3",
"protein_id": "XP_016878378.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 340,
"cds_start": 487,
"cds_end": null,
"cds_length": 1023,
"cdna_start": 683,
"cdna_end": null,
"cdna_length": 1253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "n.487C>T",
"hgvs_p": null,
"transcript": "ENST00000636131.1",
"protein_id": "ENSP00000490390.1",
"transcript_support_level": 5,
"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": 2365,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.339+148C>T",
"hgvs_p": null,
"transcript": "ENST00000637565.1",
"protein_id": "ENSP00000490207.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "c.339+148C>T",
"hgvs_p": null,
"transcript": "ENST00000567551.2",
"protein_id": "ENSP00000489813.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": -4,
"cds_end": null,
"cds_length": 436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MVP-DT",
"gene_hgnc_id": 56029,
"hgvs_c": "n.246-3368G>A",
"hgvs_p": null,
"transcript": "ENST00000569039.5",
"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": 589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "n.88-145C>T",
"hgvs_p": null,
"transcript": "ENST00000636019.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PRRT2",
"gene_hgnc_id": 30500,
"hgvs_c": "n.340-145C>T",
"hgvs_p": null,
"transcript": "ENST00000637290.1",
"protein_id": "ENSP00000490278.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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}
],
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"computational_score_selected": 0.5199999809265137,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
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"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.771,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
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"pathogenic_score": 12,
"criteria": [
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"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000358758.12",
"gene_symbol": "PRRT2",
"hgnc_id": 30500,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.487C>T",
"hgvs_p": "p.Gln163*"
},
{
"score": 8,
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"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000609618.2",
"gene_symbol": "ENSG00000280893",
"hgnc_id": null,
"effects": [
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],
"inheritance_mode": "",
"hgvs_c": "n.487C>T",
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},
{
"score": 8,
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"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000569039.5",
"gene_symbol": "MVP-DT",
"hgnc_id": 56029,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.246-3368G>A",
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}
],
"clinvar_disease": "Episodic kinesigenic dyskinesia 1,Inborn genetic diseases,Infantile convulsions and choreoathetosis",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Episodic kinesigenic dyskinesia 1|Infantile convulsions and choreoathetosis|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}