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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: X-71169881-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=71169881&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 71169881,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_181303.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2331C>T",
"hgvs_p": "p.Ala777Ala",
"transcript": "NM_181303.2",
"protein_id": "NP_851820.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 848,
"cds_start": 2331,
"cds_end": null,
"cds_length": 2547,
"cdna_start": 2655,
"cdna_end": null,
"cdna_length": 3975,
"mane_select": "ENST00000358741.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2331C>T",
"hgvs_p": "p.Ala777Ala",
"transcript": "ENST00000358741.4",
"protein_id": "ENSP00000351591.4",
"transcript_support_level": 5,
"aa_start": 777,
"aa_end": null,
"aa_length": 848,
"cds_start": 2331,
"cds_end": null,
"cds_length": 2547,
"cdna_start": 2655,
"cdna_end": null,
"cdna_length": 3975,
"mane_select": "NM_181303.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2271C>T",
"hgvs_p": "p.Ala757Ala",
"transcript": "ENST00000374051.7",
"protein_id": "ENSP00000363163.3",
"transcript_support_level": 1,
"aa_start": 757,
"aa_end": null,
"aa_length": 828,
"cds_start": 2271,
"cds_end": null,
"cds_length": 2487,
"cdna_start": 2593,
"cdna_end": null,
"cdna_length": 3913,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "n.2510C>T",
"hgvs_p": null,
"transcript": "ENST00000476589.2",
"protein_id": null,
"transcript_support_level": 1,
"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": 3789,
"mane_select": null,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "n.*1678C>T",
"hgvs_p": null,
"transcript": "ENST00000685718.1",
"protein_id": "ENSP00000510514.1",
"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": 4125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "n.*1678C>T",
"hgvs_p": null,
"transcript": "ENST00000685718.1",
"protein_id": "ENSP00000510514.1",
"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": 4125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2271C>T",
"hgvs_p": "p.Ala757Ala",
"transcript": "NM_018977.4",
"protein_id": "NP_061850.2",
"transcript_support_level": null,
"aa_start": 757,
"aa_end": null,
"aa_length": 828,
"cds_start": 2271,
"cds_end": null,
"cds_length": 2487,
"cdna_start": 2595,
"cdna_end": null,
"cdna_length": 3915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2211C>T",
"hgvs_p": "p.Ala737Ala",
"transcript": "NM_001166660.2",
"protein_id": "NP_001160132.1",
"transcript_support_level": null,
"aa_start": 737,
"aa_end": null,
"aa_length": 808,
"cds_start": 2211,
"cds_end": null,
"cds_length": 2427,
"cdna_start": 2535,
"cdna_end": null,
"cdna_length": 3855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2211C>T",
"hgvs_p": "p.Ala737Ala",
"transcript": "ENST00000536169.6",
"protein_id": "ENSP00000445298.1",
"transcript_support_level": 5,
"aa_start": 737,
"aa_end": null,
"aa_length": 808,
"cds_start": 2211,
"cds_end": null,
"cds_length": 2427,
"cdna_start": 2533,
"cdna_end": null,
"cdna_length": 3812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2061C>T",
"hgvs_p": "p.Ala687Ala",
"transcript": "ENST00000689857.1",
"protein_id": "ENSP00000510719.1",
"transcript_support_level": null,
"aa_start": 687,
"aa_end": null,
"aa_length": 758,
"cds_start": 2061,
"cds_end": null,
"cds_length": 2277,
"cdna_start": 2405,
"cdna_end": null,
"cdna_length": 3670,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1992C>T",
"hgvs_p": "p.Ala664Ala",
"transcript": "ENST00000689968.1",
"protein_id": "ENSP00000510150.1",
"transcript_support_level": null,
"aa_start": 664,
"aa_end": null,
"aa_length": 735,
"cds_start": 1992,
"cds_end": null,
"cds_length": 2208,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 3512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1980C>T",
"hgvs_p": "p.Ala660Ala",
"transcript": "NM_001437941.1",
"protein_id": "NP_001424870.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 731,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 2142,
"cdna_end": null,
"cdna_length": 3462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1980C>T",
"hgvs_p": "p.Ala660Ala",
"transcript": "NM_001438296.1",
"protein_id": "NP_001425225.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 731,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 2220,
"cdna_end": null,
"cdna_length": 3540,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1980C>T",
"hgvs_p": "p.Ala660Ala",
"transcript": "ENST00000687220.1",
"protein_id": "ENSP00000509531.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 731,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 2215,
"cdna_end": null,
"cdna_length": 3494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1980C>T",
"hgvs_p": "p.Ala660Ala",
"transcript": "ENST00000688566.1",
"protein_id": "ENSP00000509202.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 731,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2196,
"cdna_start": 2140,
"cdna_end": null,
"cdna_length": 3419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1920C>T",
"hgvs_p": "p.Ala640Ala",
"transcript": "NM_001321276.2",
"protein_id": "NP_001308205.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 711,
"cds_start": 1920,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2082,
"cdna_end": null,
"cdna_length": 3402,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1920C>T",
"hgvs_p": "p.Ala640Ala",
"transcript": "NM_001438298.1",
"protein_id": "NP_001425227.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 711,
"cds_start": 1920,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2160,
"cdna_end": null,
"cdna_length": 3480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1920C>T",
"hgvs_p": "p.Ala640Ala",
"transcript": "ENST00000690133.1",
"protein_id": "ENSP00000508912.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 711,
"cds_start": 1920,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2129,
"cdna_end": null,
"cdna_length": 3408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.1920C>T",
"hgvs_p": "p.Ala640Ala",
"transcript": "ENST00000692338.1",
"protein_id": "ENSP00000508700.1",
"transcript_support_level": null,
"aa_start": 640,
"aa_end": null,
"aa_length": 711,
"cds_start": 1920,
"cds_end": null,
"cds_length": 2136,
"cdna_start": 2062,
"cdna_end": null,
"cdna_length": 3341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2331C>T",
"hgvs_p": "p.Ala777Ala",
"transcript": "XM_047442185.1",
"protein_id": "XP_047298141.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 848,
"cds_start": 2331,
"cds_end": null,
"cds_length": 2547,
"cdna_start": 2913,
"cdna_end": null,
"cdna_length": 4233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "c.2184C>T",
"hgvs_p": "p.Ala728Ala",
"transcript": "XM_006724662.5",
"protein_id": "XP_006724725.2",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 799,
"cds_start": 2184,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 2477,
"cdna_end": null,
"cdna_length": 3797,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "n.4006C>T",
"hgvs_p": null,
"transcript": "ENST00000685950.1",
"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": 5193,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NLGN3",
"gene_hgnc_id": 14289,
"hgvs_c": "n.3314C>T",
"hgvs_p": null,
"transcript": "ENST00000688950.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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},
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},
{
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{
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},
{
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{
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{
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{
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},
{
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}
],
"gene_symbol": "NLGN3",
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"dbsnp": "rs759656254",
"frequency_reference_population": 0.00007605637,
"hom_count_reference_population": 52,
"allele_count_reference_population": 91,
"gnomad_exomes_af": 0.0000810445,
"gnomad_genomes_af": 0.0000271106,
"gnomad_exomes_ac": 88,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7599999904632568,
"computational_prediction_selected": "Benign",
"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,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.142,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_181303.2",
"gene_symbol": "NLGN3",
"hgnc_id": 14289,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,XL",
"hgvs_c": "c.2331C>T",
"hgvs_p": "p.Ala777Ala"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000740246.1",
"gene_symbol": "ENSG00000228427",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.346+14030G>A",
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}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}