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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: 2-110146839-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=110146839&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 110146839,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000445609.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1270-4C>T",
"hgvs_p": null,
"transcript": "NM_001128178.3",
"protein_id": "NP_001121650.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 677,
"cds_start": -4,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": "ENST00000445609.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1270-4C>T",
"hgvs_p": null,
"transcript": "ENST00000445609.7",
"protein_id": "ENSP00000389879.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 677,
"cds_start": -4,
"cds_end": null,
"cds_length": 2034,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2522,
"mane_select": "NM_001128178.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1438-4C>T",
"hgvs_p": null,
"transcript": "ENST00000316534.8",
"protein_id": "ENSP00000313169.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 733,
"cds_start": -4,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1435-4C>T",
"hgvs_p": null,
"transcript": "ENST00000393272.7",
"protein_id": "ENSP00000376953.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1081-4C>T",
"hgvs_p": null,
"transcript": "ENST00000355301.8",
"protein_id": "ENSP00000347452.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 614,
"cds_start": -4,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1438-4C>T",
"hgvs_p": null,
"transcript": "NM_000272.5",
"protein_id": "NP_000263.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 733,
"cds_start": -4,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1435-4C>T",
"hgvs_p": null,
"transcript": "NM_207181.4",
"protein_id": "NP_997064.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1267-4C>T",
"hgvs_p": null,
"transcript": "ENST00000417665.5",
"protein_id": "ENSP00000402176.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 711,
"cds_start": -4,
"cds_end": null,
"cds_length": 2136,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1267-4C>T",
"hgvs_p": null,
"transcript": "NM_001374256.1",
"protein_id": "NP_001361185.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 676,
"cds_start": -4,
"cds_end": null,
"cds_length": 2031,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1270-4C>T",
"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": -4,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1087-4C>T",
"hgvs_p": null,
"transcript": "ENST00000676028.1",
"protein_id": "ENSP00000502639.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 616,
"cds_start": -4,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1081-4C>T",
"hgvs_p": null,
"transcript": "NM_001128179.3",
"protein_id": "NP_001121651.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 614,
"cds_start": -4,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2333,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1081-4C>T",
"hgvs_p": null,
"transcript": "ENST00000676053.1",
"protein_id": "ENSP00000502475.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 614,
"cds_start": -4,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.1315-4C>T",
"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": -4,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.469-4C>T",
"hgvs_p": null,
"transcript": "ENST00000675067.1",
"protein_id": "ENSP00000502817.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 410,
"cds_start": -4,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "c.466-4C>T",
"hgvs_p": null,
"transcript": "ENST00000676091.1",
"protein_id": "ENSP00000502528.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 409,
"cds_start": -4,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1313,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.2855-4C>T",
"hgvs_p": null,
"transcript": "ENST00000461707.5",
"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": 3822,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.2871-4C>T",
"hgvs_p": null,
"transcript": "ENST00000496524.5",
"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": 10006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.1948-4C>T",
"hgvs_p": null,
"transcript": "ENST00000675356.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 3065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.2674-4C>T",
"hgvs_p": null,
"transcript": "ENST00000675632.1",
"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": 3791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.2973-4C>T",
"hgvs_p": null,
"transcript": "ENST00000675752.1",
"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": 4078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"hgvs_c": "n.2933-4C>T",
"hgvs_p": null,
"transcript": "ENST00000676165.1",
"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": 4050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "NPHP1",
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{
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"intron_variant"
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"exon_count": 21,
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},
{
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"protein_coding": true,
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},
{
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"gene_symbol": "NPHP1",
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"hgvs_c": "c.1270-4C>T",
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"transcript": "XM_005263676.2",
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},
{
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"gene_symbol": "NPHP1",
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"hgvs_c": "c.1267-4C>T",
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"cdna_length": 2624,
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"feature": null
}
],
"gene_symbol": "NPHP1",
"gene_hgnc_id": 7905,
"dbsnp": "rs151204566",
"frequency_reference_population": 0.0025843037,
"hom_count_reference_population": 22,
"allele_count_reference_population": 4158,
"gnomad_exomes_af": 0.00266481,
"gnomad_genomes_af": 0.00181367,
"gnomad_exomes_ac": 3882,
"gnomad_genomes_ac": 276,
"gnomad_exomes_homalt": 20,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.02199999988079071,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.472,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000844395570429258,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000445609.7",
"gene_symbol": "NPHP1",
"hgnc_id": 7905,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1270-4C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome with renal defect,Nephronophthisis,Nephronophthisis 1,Senior-Loken syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:4 B:1",
"phenotype_combined": "not specified|Nephronophthisis|Senior-Loken syndrome 1|Joubert syndrome with renal defect|not provided|Nephronophthisis 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}