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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: 19-49861765-ACGCTACCTGG-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49861765&ref=ACGCTACCTGG&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 49861765,
"ref": "ACGCTACCTGG",
"alt": "A",
"effect": "frameshift_variant,splice_donor_variant,splice_region_variant,intron_variant",
"transcript": "NM_007254.4",
"consequences": [
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs",
"transcript": "NM_007254.4",
"protein_id": "NP_009185.2",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 521,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000322344.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007254.4"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs",
"transcript": "ENST00000322344.8",
"protein_id": "ENSP00000323511.2",
"transcript_support_level": 1,
"aa_start": 432,
"aa_end": null,
"aa_length": 521,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007254.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322344.8"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs",
"transcript": "ENST00000596014.5",
"protein_id": "ENSP00000472300.1",
"transcript_support_level": 1,
"aa_start": 432,
"aa_end": null,
"aa_length": 521,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596014.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1222_*1225+6delCCAGGTAGCG",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000593946.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"splice_region_variant",
"3_prime_UTR_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "n.*1222_*1225+6delCCAGGTAGCG",
"hgvs_p": null,
"transcript": "ENST00000593946.5",
"protein_id": "ENSP00000468896.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000593946.5"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1322_1325+6delCCAGGTAGCG",
"hgvs_p": "p.Ala441fs",
"transcript": "ENST00000861313.1",
"protein_id": "ENSP00000531372.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 530,
"cds_start": 1322,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861313.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1322_1325+6delCCAGGTAGCG",
"hgvs_p": "p.Ala441fs",
"transcript": "ENST00000934451.1",
"protein_id": "ENSP00000604510.1",
"transcript_support_level": null,
"aa_start": 441,
"aa_end": null,
"aa_length": 530,
"cds_start": 1322,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934451.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs",
"transcript": "ENST00000934445.1",
"protein_id": "ENSP00000604504.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 521,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934445.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs",
"transcript": "ENST00000934450.1",
"protein_id": "ENSP00000604509.1",
"transcript_support_level": null,
"aa_start": 432,
"aa_end": null,
"aa_length": 521,
"cds_start": 1295,
"cds_end": null,
"cds_length": 1566,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934450.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1274_1277+6delCCAGGTAGCG",
"hgvs_p": "p.Ala425fs",
"transcript": "ENST00000934449.1",
"protein_id": "ENSP00000604508.1",
"transcript_support_level": null,
"aa_start": 425,
"aa_end": null,
"aa_length": 514,
"cds_start": 1274,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934449.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1262_1265+6delCCAGGTAGCG",
"hgvs_p": "p.Ala421fs",
"transcript": "ENST00000965095.1",
"protein_id": "ENSP00000635154.1",
"transcript_support_level": null,
"aa_start": 421,
"aa_end": null,
"aa_length": 510,
"cds_start": 1262,
"cds_end": null,
"cds_length": 1533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965095.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1256_1259+6delCCAGGTAGCG",
"hgvs_p": "p.Ala419fs",
"transcript": "ENST00000934448.1",
"protein_id": "ENSP00000604507.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 508,
"cds_start": 1256,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934448.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1253_1256+6delCCAGGTAGCG",
"hgvs_p": "p.Ala418fs",
"transcript": "ENST00000861311.1",
"protein_id": "ENSP00000531370.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 507,
"cds_start": 1253,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861311.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1202_1205+6delCCAGGTAGCG",
"hgvs_p": "p.Ala401fs",
"transcript": "ENST00000600573.5",
"protein_id": "ENSP00000469826.1",
"transcript_support_level": 5,
"aa_start": 401,
"aa_end": null,
"aa_length": 490,
"cds_start": 1202,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600573.5"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1187_1190+6delCCAGGTAGCG",
"hgvs_p": "p.Ala396fs",
"transcript": "ENST00000631020.2",
"protein_id": "ENSP00000486707.1",
"transcript_support_level": 5,
"aa_start": 396,
"aa_end": null,
"aa_length": 485,
"cds_start": 1187,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000631020.2"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1169_1172+6delCCAGGTAGCG",
"hgvs_p": "p.Ala390fs",
"transcript": "ENST00000861312.1",
"protein_id": "ENSP00000531371.1",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 479,
"cds_start": 1169,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861312.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1169_1172+6delCCAGGTAGCG",
"hgvs_p": "p.Ala390fs",
"transcript": "ENST00000965096.1",
"protein_id": "ENSP00000635155.1",
"transcript_support_level": null,
"aa_start": 390,
"aa_end": null,
"aa_length": 479,
"cds_start": 1169,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965096.1"
},
{
"aa_ref": "AR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1148_1151+6delCCAGGTAGCG",
"hgvs_p": "p.Ala383fs",
"transcript": "ENST00000965094.1",
"protein_id": "ENSP00000635153.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 472,
"cds_start": 1148,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965094.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1189-80_1189-71delCCAGGTAGCG",
"hgvs_p": null,
"transcript": "ENST00000934444.1",
"protein_id": "ENSP00000604503.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 471,
"cds_start": null,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934444.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "PNKP",
"gene_hgnc_id": 9154,
"hgvs_c": "c.1189-80_1189-71delCCAGGTAGCG",
"hgvs_p": null,
"transcript": "ENST00000600910.5",
"protein_id": "ENSP00000473137.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 455,
"cds_start": null,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600910.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
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],
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"dbsnp": "rs587784366",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 72,
"gnomad_exomes_af": 0.0000473657,
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"gnomad_exomes_ac": 67,
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"gnomad_mito_homoplasmic": null,
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"computational_source_selected": null,
"splice_score_selected": null,
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"revel_score": null,
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"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.562,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
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"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
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"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_007254.4",
"gene_symbol": "PNKP",
"hgnc_id": 9154,
"effects": [
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"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1295_1298+6delCCAGGTAGCG",
"hgvs_p": "p.Ala432fs"
}
],
"clinvar_disease": " 12, and developmental delay, early-onset, seizures, with oculomotor apraxia and hypoalbuminemia,Ataxia,Developmental and epileptic encephalopathy,Microcephaly,PNKP-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:7 LP:1",
"phenotype_combined": "Microcephaly, seizures, and developmental delay|not provided|Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia|Developmental and epileptic encephalopathy, 12|PNKP-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}