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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: 2-110123808-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=110123808&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 110123808,
"ref": "T",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "NM_000272.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2017A>C",
"hgvs_p": "p.Arg673Arg",
"transcript": "NM_001128178.3",
"protein_id": "NP_001121650.1",
"transcript_support_level": null,
"aa_start": 673,
"aa_end": null,
"aa_length": 677,
"cds_start": 2017,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": "ENST00000445609.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128178.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2017A>C",
"hgvs_p": "p.Arg673Arg",
"transcript": "ENST00000445609.7",
"protein_id": "ENSP00000389879.3",
"transcript_support_level": 1,
"aa_start": 673,
"aa_end": null,
"aa_length": 677,
"cds_start": 2017,
"cds_end": null,
"cds_length": 2034,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": "NM_001128178.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000445609.7"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2185A>C",
"hgvs_p": "p.Arg729Arg",
"transcript": "ENST00000316534.8",
"protein_id": "ENSP00000313169.4",
"transcript_support_level": 1,
"aa_start": 729,
"aa_end": null,
"aa_length": 733,
"cds_start": 2185,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2259,
"cdna_end": null,
"cdna_length": 3756,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000316534.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2182A>C",
"hgvs_p": "p.Arg728Arg",
"transcript": "ENST00000393272.7",
"protein_id": "ENSP00000376953.3",
"transcript_support_level": 1,
"aa_start": 728,
"aa_end": null,
"aa_length": 732,
"cds_start": 2182,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2280,
"cdna_end": null,
"cdna_length": 2752,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393272.7"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1828A>C",
"hgvs_p": "p.Arg610Arg",
"transcript": "ENST00000355301.8",
"protein_id": "ENSP00000347452.4",
"transcript_support_level": 1,
"aa_start": 610,
"aa_end": null,
"aa_length": 614,
"cds_start": 1828,
"cds_end": null,
"cds_length": 1845,
"cdna_start": 1832,
"cdna_end": null,
"cdna_length": 1932,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355301.8"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2218A>C",
"hgvs_p": "p.Arg740Arg",
"transcript": "ENST00000955859.1",
"protein_id": "ENSP00000625918.1",
"transcript_support_level": null,
"aa_start": 740,
"aa_end": null,
"aa_length": 744,
"cds_start": 2218,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 2271,
"cdna_end": null,
"cdna_length": 2730,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955859.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2185A>C",
"hgvs_p": "p.Arg729Arg",
"transcript": "NM_000272.5",
"protein_id": "NP_000263.2",
"transcript_support_level": null,
"aa_start": 729,
"aa_end": null,
"aa_length": 733,
"cds_start": 2185,
"cds_end": null,
"cds_length": 2202,
"cdna_start": 2230,
"cdna_end": null,
"cdna_length": 2690,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000272.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2182A>C",
"hgvs_p": "p.Arg728Arg",
"transcript": "NM_207181.4",
"protein_id": "NP_997064.2",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 732,
"cds_start": 2182,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 2227,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_207181.4"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2122A>C",
"hgvs_p": "p.Arg708Arg",
"transcript": "ENST00000866172.1",
"protein_id": "ENSP00000536231.1",
"transcript_support_level": null,
"aa_start": 708,
"aa_end": null,
"aa_length": 712,
"cds_start": 2122,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 2167,
"cdna_end": null,
"cdna_length": 2262,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866172.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2119A>C",
"hgvs_p": "p.Arg707Arg",
"transcript": "ENST00000417665.5",
"protein_id": "ENSP00000402176.1",
"transcript_support_level": 5,
"aa_start": 707,
"aa_end": null,
"aa_length": 711,
"cds_start": 2119,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2146,
"cdna_end": null,
"cdna_length": 2246,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417665.5"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2014A>C",
"hgvs_p": "p.Arg672Arg",
"transcript": "NM_001374256.1",
"protein_id": "NP_001361185.1",
"transcript_support_level": null,
"aa_start": 672,
"aa_end": null,
"aa_length": 676,
"cds_start": 2014,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 2059,
"cdna_end": null,
"cdna_length": 2519,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374256.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2002A>C",
"hgvs_p": "p.Arg668Arg",
"transcript": "ENST00000955860.1",
"protein_id": "ENSP00000625919.1",
"transcript_support_level": null,
"aa_start": 668,
"aa_end": null,
"aa_length": 672,
"cds_start": 2002,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 2040,
"cdna_end": null,
"cdna_length": 2135,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955860.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1834A>C",
"hgvs_p": "p.Arg612Arg",
"transcript": "ENST00000676028.1",
"protein_id": "ENSP00000502639.1",
"transcript_support_level": null,
"aa_start": 612,
"aa_end": null,
"aa_length": 616,
"cds_start": 1834,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676028.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1828A>C",
"hgvs_p": "p.Arg610Arg",
"transcript": "NM_001128179.3",
"protein_id": "NP_001121651.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 614,
"cds_start": 1828,
"cds_end": null,
"cds_length": 1845,
"cdna_start": 1873,
"cdna_end": null,
"cdna_length": 2333,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128179.3"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1828A>C",
"hgvs_p": "p.Arg610Arg",
"transcript": "ENST00000676053.1",
"protein_id": "ENSP00000502475.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 614,
"cds_start": 1828,
"cds_end": null,
"cds_length": 1845,
"cdna_start": 1848,
"cdna_end": null,
"cdna_length": 2218,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676053.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1216A>C",
"hgvs_p": "p.Arg406Arg",
"transcript": "ENST00000675067.1",
"protein_id": "ENSP00000502817.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 410,
"cds_start": 1216,
"cds_end": null,
"cds_length": 1233,
"cdna_start": 3515,
"cdna_end": null,
"cdna_length": 3885,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675067.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1213A>C",
"hgvs_p": "p.Arg405Arg",
"transcript": "ENST00000676091.1",
"protein_id": "ENSP00000502528.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 409,
"cds_start": 1213,
"cds_end": null,
"cds_length": 1230,
"cdna_start": 1213,
"cdna_end": null,
"cdna_length": 1313,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676091.1"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2290A>C",
"hgvs_p": "p.Arg764Arg",
"transcript": "XM_006712551.2",
"protein_id": "XP_006712614.1",
"transcript_support_level": null,
"aa_start": 764,
"aa_end": null,
"aa_length": 768,
"cds_start": 2290,
"cds_end": null,
"cds_length": 2307,
"cdna_start": 2335,
"cdna_end": null,
"cdna_length": 2795,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712551.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2122A>C",
"hgvs_p": "p.Arg708Arg",
"transcript": "XM_005263676.2",
"protein_id": "XP_005263733.1",
"transcript_support_level": null,
"aa_start": 708,
"aa_end": null,
"aa_length": 712,
"cds_start": 2122,
"cds_end": null,
"cds_length": 2139,
"cdna_start": 2167,
"cdna_end": null,
"cdna_length": 2627,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005263676.2"
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.2119A>C",
"hgvs_p": "p.Arg707Arg",
"transcript": "XM_005263677.2",
"protein_id": "XP_005263734.1",
"transcript_support_level": null,
"aa_start": 707,
"aa_end": null,
"aa_length": 711,
"cds_start": 2119,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2164,
"cdna_end": null,
"cdna_length": 2624,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005263677.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.*259A>C",
"hgvs_p": null,
"transcript": "NM_001374257.1",
"protein_id": "NP_001361186.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 630,
"cds_start": null,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374257.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.*1805A>C",
"hgvs_p": null,
"transcript": "ENST00000674677.1",
"protein_id": "ENSP00000502265.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 609,
"cds_start": null,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4034,
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{
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],
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],
"gene_symbol": "NPHP1",
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"dbsnp": "rs1679144907",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
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"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": -0.7699999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.794,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
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"mitotip_score": null,
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"acmg_score": -4,
"acmg_classification": "Likely_benign",
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"acmg_by_gene": [
{
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"pathogenic_score": 2,
"criteria": [
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"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_000272.5",
"gene_symbol": "NPHP1",
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"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
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"hgvs_p": "p.Arg729Arg"
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],
"clinvar_disease": "Nephronophthisis",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Nephronophthisis",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}