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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: 12-88083848-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88083848&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 88083848,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "NM_025114.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*",
"transcript": "NM_025114.4",
"protein_id": "NP_079390.3",
"transcript_support_level": null,
"aa_start": 1604,
"aa_end": null,
"aa_length": 2479,
"cds_start": 4811,
"cds_end": null,
"cds_length": 7440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000552810.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025114.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*",
"transcript": "ENST00000552810.6",
"protein_id": "ENSP00000448012.1",
"transcript_support_level": 1,
"aa_start": 1604,
"aa_end": null,
"aa_length": 2479,
"cds_start": 4811,
"cds_end": null,
"cds_length": 7440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_025114.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000552810.6"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.2093G>A",
"hgvs_p": "p.Trp698*",
"transcript": "ENST00000547691.8",
"protein_id": "ENSP00000446905.3",
"transcript_support_level": 1,
"aa_start": 698,
"aa_end": null,
"aa_length": 1468,
"cds_start": 2093,
"cds_end": null,
"cds_length": 4407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000547691.8"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "ENST00000675476.1",
"protein_id": "ENSP00000502161.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2766,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8301,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675476.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 37,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5579G>A",
"hgvs_p": "p.Trp1860*",
"transcript": "ENST00000675833.1",
"protein_id": "ENSP00000502559.1",
"transcript_support_level": null,
"aa_start": 1860,
"aa_end": null,
"aa_length": 2735,
"cds_start": 5579,
"cds_end": null,
"cds_length": 8208,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675833.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*",
"transcript": "ENST00000309041.12",
"protein_id": "ENSP00000308021.8",
"transcript_support_level": 5,
"aa_start": 1604,
"aa_end": null,
"aa_length": 2482,
"cds_start": 4811,
"cds_end": null,
"cds_length": 7449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000309041.12"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4790G>A",
"hgvs_p": "p.Trp1597*",
"transcript": "ENST00000675230.1",
"protein_id": "ENSP00000502503.1",
"transcript_support_level": null,
"aa_start": 1597,
"aa_end": null,
"aa_length": 2472,
"cds_start": 4790,
"cds_end": null,
"cds_length": 7419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675230.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4736G>A",
"hgvs_p": "p.Trp1579*",
"transcript": "ENST00000940537.1",
"protein_id": "ENSP00000610596.1",
"transcript_support_level": null,
"aa_start": 1579,
"aa_end": null,
"aa_length": 2454,
"cds_start": 4736,
"cds_end": null,
"cds_length": 7365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940537.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*",
"transcript": "ENST00000673058.2",
"protein_id": "ENSP00000500665.2",
"transcript_support_level": null,
"aa_start": 1604,
"aa_end": null,
"aa_length": 2438,
"cds_start": 4811,
"cds_end": null,
"cds_length": 7317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000673058.2"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*",
"transcript": "ENST00000675408.1",
"protein_id": "ENSP00000502298.1",
"transcript_support_level": null,
"aa_start": 1604,
"aa_end": null,
"aa_length": 2424,
"cds_start": 4811,
"cds_end": null,
"cds_length": 7275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675408.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.4790G>A",
"hgvs_p": "p.Trp1597*",
"transcript": "ENST00000940538.1",
"protein_id": "ENSP00000610597.1",
"transcript_support_level": null,
"aa_start": 1597,
"aa_end": null,
"aa_length": 2417,
"cds_start": 4790,
"cds_end": null,
"cds_length": 7254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940538.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538756.4",
"protein_id": "XP_011537058.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2769,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538756.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538757.4",
"protein_id": "XP_011537059.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2769,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538757.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538758.4",
"protein_id": "XP_011537060.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2768,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8307,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538758.4"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538759.3",
"protein_id": "XP_011537061.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2766,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8301,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538759.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538760.3",
"protein_id": "XP_011537062.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2728,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538760.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_017019980.3",
"protein_id": "XP_016875469.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2725,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019980.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_011538761.3",
"protein_id": "XP_011537063.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2714,
"cds_start": 5672,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011538761.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_017019981.3",
"protein_id": "XP_016875470.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2711,
"cds_start": 5672,
"cds_end": null,
"cds_length": 8136,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019981.3"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_017019982.2",
"protein_id": "XP_016875471.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2612,
"cds_start": 5672,
"cds_end": null,
"cds_length": 7839,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019982.2"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 38,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "c.5672G>A",
"hgvs_p": "p.Trp1891*",
"transcript": "XM_047429558.1",
"protein_id": "XP_047285514.1",
"transcript_support_level": null,
"aa_start": 1891,
"aa_end": null,
"aa_length": 2609,
"cds_start": 5672,
"cds_end": null,
"cds_length": 7830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429558.1"
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
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"aa_length": null,
"cds_start": null,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000675794.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"hgvs_c": "n.*2724G>A",
"hgvs_p": null,
"transcript": "ENST00000676448.1",
"protein_id": "ENSP00000501987.1",
"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": "ENST00000676448.1"
}
],
"gene_symbol": "CEP290",
"gene_hgnc_id": 29021,
"dbsnp": "rs886039808",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5899999737739563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.527999997138977,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.867,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0802004306884211,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_025114.4",
"gene_symbol": "CEP290",
"hgnc_id": 29021,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4811G>A",
"hgvs_p": "p.Trp1604*"
}
],
"clinvar_disease": "Joubert syndrome and related disorders",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Joubert syndrome and related disorders",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}