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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: 2-108470396-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=108470396&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 108470396,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_181453.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "NM_181453.4",
"protein_id": "NP_852118.2",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1684,
"cds_start": 1067,
"cds_end": null,
"cds_length": 5055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000309863.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_181453.4"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000309863.11",
"protein_id": "ENSP00000307939.5",
"transcript_support_level": 5,
"aa_start": 356,
"aa_end": null,
"aa_length": 1684,
"cds_start": 1067,
"cds_end": null,
"cds_length": 5055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_181453.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000309863.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "n.*844C>T",
"hgvs_p": null,
"transcript": "ENST00000482325.5",
"protein_id": "ENSP00000419969.1",
"transcript_support_level": 1,
"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": "ENST00000482325.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "n.*844C>T",
"hgvs_p": null,
"transcript": "ENST00000482325.5",
"protein_id": "ENSP00000419969.1",
"transcript_support_level": 1,
"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": "ENST00000482325.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000926769.1",
"protein_id": "ENSP00000596828.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1688,
"cds_start": 1067,
"cds_end": null,
"cds_length": 5067,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926769.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000926767.1",
"protein_id": "ENSP00000596826.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1682,
"cds_start": 1067,
"cds_end": null,
"cds_length": 5049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926767.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000687399.1",
"protein_id": "ENSP00000509332.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1638,
"cds_start": 1067,
"cds_end": null,
"cds_length": 4917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000687399.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.914C>T",
"hgvs_p": "p.Thr305Ile",
"transcript": "ENST00000692694.1",
"protein_id": "ENSP00000509242.1",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 1633,
"cds_start": 914,
"cds_end": null,
"cds_length": 4902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000692694.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000926766.1",
"protein_id": "ENSP00000596825.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1629,
"cds_start": 1067,
"cds_end": null,
"cds_length": 4890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926766.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.764C>T",
"hgvs_p": "p.Thr255Ile",
"transcript": "NM_001410194.1",
"protein_id": "NP_001397123.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 1583,
"cds_start": 764,
"cds_end": null,
"cds_length": 4752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410194.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.764C>T",
"hgvs_p": "p.Thr255Ile",
"transcript": "ENST00000685519.1",
"protein_id": "ENSP00000508981.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 1583,
"cds_start": 764,
"cds_end": null,
"cds_length": 4752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000685519.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "ENST00000953175.1",
"protein_id": "ENSP00000623234.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 1399,
"cds_start": 1067,
"cds_end": null,
"cds_length": 4200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953175.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.956C>T",
"hgvs_p": "p.Thr319Ile",
"transcript": "ENST00000409896.1",
"protein_id": "ENSP00000386997.1",
"transcript_support_level": 5,
"aa_start": 319,
"aa_end": null,
"aa_length": 915,
"cds_start": 956,
"cds_end": null,
"cds_length": 2749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409896.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Thr359Ile",
"transcript": "XM_006712870.4",
"protein_id": "XP_006712933.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 1687,
"cds_start": 1076,
"cds_end": null,
"cds_length": 5064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712870.4"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.764C>T",
"hgvs_p": "p.Thr255Ile",
"transcript": "XM_006712871.2",
"protein_id": "XP_006712934.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 1583,
"cds_start": 764,
"cds_end": null,
"cds_length": 4752,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712871.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Thr359Ile",
"transcript": "XM_047446447.1",
"protein_id": "XP_047302403.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 1320,
"cds_start": 1076,
"cds_end": null,
"cds_length": 3963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446447.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Thr359Ile",
"transcript": "XM_047446448.1",
"protein_id": "XP_047302404.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 1257,
"cds_start": 1076,
"cds_end": null,
"cds_length": 3774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446448.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Thr359Ile",
"transcript": "XM_006712872.4",
"protein_id": "XP_006712935.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 977,
"cds_start": 1076,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006712872.4"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile",
"transcript": "XM_047446449.1",
"protein_id": "XP_047302405.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 974,
"cds_start": 1067,
"cds_end": null,
"cds_length": 2925,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446449.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "c.217-2431C>T",
"hgvs_p": null,
"transcript": "ENST00000926768.1",
"protein_id": "ENSP00000596827.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 831,
"cds_start": null,
"cds_end": null,
"cds_length": 2496,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926768.1"
},
{
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "n.1530C>T",
"hgvs_p": null,
"transcript": "ENST00000687832.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000687832.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GCC2",
"gene_hgnc_id": 23218,
"hgvs_c": "n.1223C>T",
"hgvs_p": null,
"transcript": "ENST00000688612.1",
"protein_id": null,
"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,
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{
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{
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],
"gene_symbol": "GCC2",
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"dbsnp": "rs765826004",
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"hom_count_reference_population": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04002097249031067,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.111,
"revel_prediction": "Benign",
"alphamissense_score": 0.2107,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.028,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_181453.4",
"gene_symbol": "GCC2",
"hgnc_id": 23218,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1067C>T",
"hgvs_p": "p.Thr356Ile"
},
{
"score": -4,
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"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000722733.1",
"gene_symbol": "GCC2-AS1",
"hgnc_id": 28126,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.370-5431G>A",
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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
}