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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: 3-49109046-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49109046&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49109046,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "NM_001199161.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3869G>A",
"hgvs_p": "p.Arg1290Gln",
"transcript": "ENST00000398888.6",
"protein_id": "ENSP00000381863.2",
"transcript_support_level": 1,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1318,
"cds_start": 3869,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 4188,
"cdna_end": null,
"cdna_length": 4559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4039-518G>A",
"hgvs_p": null,
"transcript": "NM_001199161.2",
"protein_id": "NP_001186090.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1384,
"cds_start": -4,
"cds_end": null,
"cds_length": 4155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4721,
"mane_select": "ENST00000417901.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4039-518G>A",
"hgvs_p": null,
"transcript": "ENST00000417901.6",
"protein_id": "ENSP00000395260.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1384,
"cds_start": -4,
"cds_end": null,
"cds_length": 4155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4721,
"mane_select": "NM_001199161.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3691-518G>A",
"hgvs_p": null,
"transcript": "ENST00000398896.6",
"protein_id": "ENSP00000381870.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1268,
"cds_start": -4,
"cds_end": null,
"cds_length": 3807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4178G>A",
"hgvs_p": "p.Arg1393Gln",
"transcript": "NM_001389594.1",
"protein_id": "NP_001376523.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1421,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 4382,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4178G>A",
"hgvs_p": "p.Arg1393Gln",
"transcript": "NM_001389595.1",
"protein_id": "NP_001376524.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1421,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 4382,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4178G>A",
"hgvs_p": "p.Arg1393Gln",
"transcript": "NM_001400288.1",
"protein_id": "NP_001387217.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1421,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 4670,
"cdna_end": null,
"cdna_length": 5043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4178G>A",
"hgvs_p": "p.Arg1393Gln",
"transcript": "ENST00000692912.1",
"protein_id": "ENSP00000508993.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1421,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 4382,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4175G>A",
"hgvs_p": "p.Arg1392Gln",
"transcript": "NM_001351100.2",
"protein_id": "NP_001338029.1",
"transcript_support_level": null,
"aa_start": 1392,
"aa_end": null,
"aa_length": 1420,
"cds_start": 4175,
"cds_end": null,
"cds_length": 4263,
"cdna_start": 4379,
"cdna_end": null,
"cdna_length": 4752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4172G>A",
"hgvs_p": "p.Arg1391Gln",
"transcript": "NM_001199160.2",
"protein_id": "NP_001186089.1",
"transcript_support_level": null,
"aa_start": 1391,
"aa_end": null,
"aa_length": 1419,
"cds_start": 4172,
"cds_end": null,
"cds_length": 4260,
"cdna_start": 4376,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4172G>A",
"hgvs_p": "p.Arg1391Gln",
"transcript": "ENST00000434032.6",
"protein_id": "ENSP00000401197.2",
"transcript_support_level": 2,
"aa_start": 1391,
"aa_end": null,
"aa_length": 1419,
"cds_start": 4172,
"cds_end": null,
"cds_length": 4260,
"cdna_start": 4384,
"cdna_end": null,
"cdna_length": 4677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4169G>A",
"hgvs_p": "p.Arg1390Gln",
"transcript": "NM_001389602.1",
"protein_id": "NP_001376531.1",
"transcript_support_level": null,
"aa_start": 1390,
"aa_end": null,
"aa_length": 1418,
"cds_start": 4169,
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"cds_length": 4257,
"cdna_start": 4373,
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"cdna_length": 4746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4133G>A",
"hgvs_p": "p.Arg1378Gln",
"transcript": "NM_001389603.1",
"protein_id": "NP_001376532.1",
"transcript_support_level": null,
"aa_start": 1378,
"aa_end": null,
"aa_length": 1406,
"cds_start": 4133,
"cds_end": null,
"cds_length": 4221,
"cdna_start": 4337,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4133G>A",
"hgvs_p": "p.Arg1378Gln",
"transcript": "ENST00000306026.6",
"protein_id": "ENSP00000303503.6",
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"cds_start": 4133,
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"cdna_start": 4332,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4127G>A",
"hgvs_p": "p.Arg1376Gln",
"transcript": "NM_001389601.1",
"protein_id": "NP_001376530.1",
"transcript_support_level": null,
"aa_start": 1376,
"aa_end": null,
"aa_length": 1404,
"cds_start": 4127,
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"cdna_start": 4331,
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"cdna_length": 4704,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4022G>A",
"hgvs_p": "p.Arg1341Gln",
"transcript": "NM_001351105.2",
"protein_id": "NP_001338034.1",
"transcript_support_level": null,
"aa_start": 1341,
"aa_end": null,
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"mane_select": null,
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"feature": null
},
{
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"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.4022G>A",
"hgvs_p": "p.Arg1341Gln",
"transcript": "ENST00000689715.1",
"protein_id": "ENSP00000510256.1",
"transcript_support_level": null,
"aa_start": 1341,
"aa_end": null,
"aa_length": 1369,
"cds_start": 4022,
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"cdna_start": 4226,
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"cdna_length": 4573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3959G>A",
"hgvs_p": "p.Arg1320Gln",
"transcript": "ENST00000698200.1",
"protein_id": "ENSP00000513604.2",
"transcript_support_level": null,
"aa_start": 1320,
"aa_end": null,
"aa_length": 1348,
"cds_start": 3959,
"cds_end": null,
"cds_length": 4047,
"cdna_start": 4188,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3881G>A",
"hgvs_p": "p.Arg1294Gln",
"transcript": "NM_001389597.1",
"protein_id": "NP_001376526.1",
"transcript_support_level": null,
"aa_start": 1294,
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"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3875G>A",
"hgvs_p": "p.Arg1292Gln",
"transcript": "NM_001389606.1",
"protein_id": "NP_001376535.1",
"transcript_support_level": null,
"aa_start": 1292,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3869G>A",
"hgvs_p": "p.Arg1290Gln",
"transcript": "NM_006677.3",
"protein_id": "NP_006668.1",
"transcript_support_level": null,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1318,
"cds_start": 3869,
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"cdna_start": 4073,
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"cdna_length": 4446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3830G>A",
"hgvs_p": "p.Arg1277Gln",
"transcript": "NM_001389607.1",
"protein_id": "NP_001376536.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 1305,
"cds_start": 3830,
"cds_end": null,
"cds_length": 3918,
"cdna_start": 4034,
"cdna_end": null,
"cdna_length": 4407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
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"frequency_reference_population": 0.000011780608,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000109549,
"gnomad_genomes_af": 0.0000197003,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2533147931098938,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.205,
"revel_prediction": "Benign",
"alphamissense_score": 0.1323,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.251,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001199161.2",
"gene_symbol": "USP19",
"hgnc_id": 12617,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4039-518G>A",
"hgvs_p": null
}
],
"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
}