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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: 3-49284048-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49284048&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49284048,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003363.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2479C>T",
"hgvs_p": "p.Arg827Cys",
"transcript": "NM_003363.4",
"protein_id": "NP_003354.2",
"transcript_support_level": null,
"aa_start": 827,
"aa_end": null,
"aa_length": 963,
"cds_start": 2479,
"cds_end": null,
"cds_length": 2892,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000265560.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003363.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2479C>T",
"hgvs_p": "p.Arg827Cys",
"transcript": "ENST00000265560.9",
"protein_id": "ENSP00000265560.4",
"transcript_support_level": 1,
"aa_start": 827,
"aa_end": null,
"aa_length": 963,
"cds_start": 2479,
"cds_end": null,
"cds_length": 2892,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003363.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265560.9"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2338C>T",
"hgvs_p": "p.Arg780Cys",
"transcript": "ENST00000351842.8",
"protein_id": "ENSP00000341028.4",
"transcript_support_level": 1,
"aa_start": 780,
"aa_end": null,
"aa_length": 916,
"cds_start": 2338,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000351842.8"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2632C>T",
"hgvs_p": "p.Arg878Cys",
"transcript": "ENST00000911610.1",
"protein_id": "ENSP00000581669.1",
"transcript_support_level": null,
"aa_start": 878,
"aa_end": null,
"aa_length": 1014,
"cds_start": 2632,
"cds_end": null,
"cds_length": 3045,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911610.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2608C>T",
"hgvs_p": "p.Arg870Cys",
"transcript": "ENST00000965332.1",
"protein_id": "ENSP00000635391.1",
"transcript_support_level": null,
"aa_start": 870,
"aa_end": null,
"aa_length": 1006,
"cds_start": 2608,
"cds_end": null,
"cds_length": 3021,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965332.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2590C>T",
"hgvs_p": "p.Arg864Cys",
"transcript": "ENST00000965340.1",
"protein_id": "ENSP00000635399.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 1000,
"cds_start": 2590,
"cds_end": null,
"cds_length": 3003,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965340.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2557C>T",
"hgvs_p": "p.Arg853Cys",
"transcript": "ENST00000877491.1",
"protein_id": "ENSP00000547550.1",
"transcript_support_level": null,
"aa_start": 853,
"aa_end": null,
"aa_length": 989,
"cds_start": 2557,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877491.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2500C>T",
"hgvs_p": "p.Arg834Cys",
"transcript": "ENST00000965341.1",
"protein_id": "ENSP00000635400.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 970,
"cds_start": 2500,
"cds_end": null,
"cds_length": 2913,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965341.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2491C>T",
"hgvs_p": "p.Arg831Cys",
"transcript": "ENST00000911611.1",
"protein_id": "ENSP00000581670.1",
"transcript_support_level": null,
"aa_start": 831,
"aa_end": null,
"aa_length": 967,
"cds_start": 2491,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911611.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2476C>T",
"hgvs_p": "p.Arg826Cys",
"transcript": "ENST00000911612.1",
"protein_id": "ENSP00000581671.1",
"transcript_support_level": null,
"aa_start": 826,
"aa_end": null,
"aa_length": 962,
"cds_start": 2476,
"cds_end": null,
"cds_length": 2889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911612.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2476C>T",
"hgvs_p": "p.Arg826Cys",
"transcript": "ENST00000965324.1",
"protein_id": "ENSP00000635383.1",
"transcript_support_level": null,
"aa_start": 826,
"aa_end": null,
"aa_length": 962,
"cds_start": 2476,
"cds_end": null,
"cds_length": 2889,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965324.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2473C>T",
"hgvs_p": "p.Arg825Cys",
"transcript": "ENST00000877475.1",
"protein_id": "ENSP00000547534.1",
"transcript_support_level": null,
"aa_start": 825,
"aa_end": null,
"aa_length": 961,
"cds_start": 2473,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877475.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2446C>T",
"hgvs_p": "p.Arg816Cys",
"transcript": "ENST00000877488.1",
"protein_id": "ENSP00000547547.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 952,
"cds_start": 2446,
"cds_end": null,
"cds_length": 2859,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877488.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2437C>T",
"hgvs_p": "p.Arg813Cys",
"transcript": "ENST00000965327.1",
"protein_id": "ENSP00000635386.1",
"transcript_support_level": null,
"aa_start": 813,
"aa_end": null,
"aa_length": 949,
"cds_start": 2437,
"cds_end": null,
"cds_length": 2850,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965327.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2425C>T",
"hgvs_p": "p.Arg809Cys",
"transcript": "ENST00000877477.1",
"protein_id": "ENSP00000547536.1",
"transcript_support_level": null,
"aa_start": 809,
"aa_end": null,
"aa_length": 945,
"cds_start": 2425,
"cds_end": null,
"cds_length": 2838,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877477.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2410C>T",
"hgvs_p": "p.Arg804Cys",
"transcript": "ENST00000965330.1",
"protein_id": "ENSP00000635389.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 940,
"cds_start": 2410,
"cds_end": null,
"cds_length": 2823,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965330.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2365C>T",
"hgvs_p": "p.Arg789Cys",
"transcript": "ENST00000877480.1",
"protein_id": "ENSP00000547539.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 925,
"cds_start": 2365,
"cds_end": null,
"cds_length": 2778,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877480.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2338C>T",
"hgvs_p": "p.Arg780Cys",
"transcript": "NM_199443.3",
"protein_id": "NP_955475.1",
"transcript_support_level": null,
"aa_start": 780,
"aa_end": null,
"aa_length": 916,
"cds_start": 2338,
"cds_end": null,
"cds_length": 2751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_199443.3"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2335C>T",
"hgvs_p": "p.Arg779Cys",
"transcript": "ENST00000877484.1",
"protein_id": "ENSP00000547543.1",
"transcript_support_level": null,
"aa_start": 779,
"aa_end": null,
"aa_length": 915,
"cds_start": 2335,
"cds_end": null,
"cds_length": 2748,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877484.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2332C>T",
"hgvs_p": "p.Arg778Cys",
"transcript": "ENST00000877485.1",
"protein_id": "ENSP00000547544.1",
"transcript_support_level": null,
"aa_start": 778,
"aa_end": null,
"aa_length": 914,
"cds_start": 2332,
"cds_end": null,
"cds_length": 2745,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877485.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2320C>T",
"hgvs_p": "p.Arg774Cys",
"transcript": "ENST00000877473.1",
"protein_id": "ENSP00000547532.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 910,
"cds_start": 2320,
"cds_end": null,
"cds_length": 2733,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877473.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP4",
"gene_hgnc_id": 12627,
"hgvs_c": "c.2305C>T",
"hgvs_p": "p.Arg769Cys",
"transcript": "ENST00000877492.1",
"protein_id": "ENSP00000547551.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 905,
"cds_start": 2305,
"cds_end": null,
"cds_length": 2718,
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{
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{
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{
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{
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],
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"biotype": "retained_intron",
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],
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"dbsnp": "rs186545761",
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"hom_count_reference_population": 0,
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"computational_score_selected": 0.9381352663040161,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"revel_prediction": "Pathogenic",
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"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.021,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
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"apogee2_prediction": null,
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"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
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"criteria": [
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"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003363.4",
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"effects": [
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"inheritance_mode": "AR",
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],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}