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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: 5-112840621-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=112840621&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 112840621,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000257430.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "NM_000038.6",
"protein_id": "NP_000029.2",
"transcript_support_level": null,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5086,
"cdna_end": null,
"cdna_length": 10704,
"mane_select": "ENST00000257430.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "ENST00000257430.9",
"protein_id": "ENSP00000257430.4",
"transcript_support_level": 5,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5086,
"cdna_end": null,
"cdna_length": 10704,
"mane_select": "NM_000038.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "ENST00000508376.6",
"protein_id": "ENSP00000427089.2",
"transcript_support_level": 1,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5184,
"cdna_end": null,
"cdna_length": 10619,
"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": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "n.*4349G>C",
"hgvs_p": null,
"transcript": "ENST00000508624.5",
"protein_id": "ENSP00000424265.1",
"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": 7406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "n.*4349G>C",
"hgvs_p": null,
"transcript": "ENST00000508624.5",
"protein_id": "ENSP00000424265.1",
"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": 7406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258864",
"gene_hgnc_id": null,
"hgvs_c": "n.228+11649G>C",
"hgvs_p": null,
"transcript": "ENST00000520401.1",
"protein_id": "ENSP00000454861.1",
"transcript_support_level": 3,
"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": 694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5111G>C",
"hgvs_p": "p.Arg1704Thr",
"transcript": "NM_001407446.1",
"protein_id": "NP_001394375.1",
"transcript_support_level": null,
"aa_start": 1704,
"aa_end": null,
"aa_length": 2871,
"cds_start": 5111,
"cds_end": null,
"cds_length": 8616,
"cdna_start": 5331,
"cdna_end": null,
"cdna_length": 10949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5081G>C",
"hgvs_p": "p.Arg1694Thr",
"transcript": "NM_001354896.2",
"protein_id": "NP_001341825.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2861,
"cds_start": 5081,
"cds_end": null,
"cds_length": 8586,
"cdna_start": 5140,
"cdna_end": null,
"cdna_length": 10758,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5081G>C",
"hgvs_p": "p.Arg1694Thr",
"transcript": "NM_001407447.1",
"protein_id": "NP_001394376.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2861,
"cds_start": 5081,
"cds_end": null,
"cds_length": 8586,
"cdna_start": 5484,
"cdna_end": null,
"cdna_length": 11102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5081G>C",
"hgvs_p": "p.Arg1694Thr",
"transcript": "NM_001407448.1",
"protein_id": "NP_001394377.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2861,
"cds_start": 5081,
"cds_end": null,
"cds_length": 8586,
"cdna_start": 5251,
"cdna_end": null,
"cdna_length": 10869,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5081G>C",
"hgvs_p": "p.Arg1694Thr",
"transcript": "NM_001407449.1",
"protein_id": "NP_001394378.1",
"transcript_support_level": null,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2861,
"cds_start": 5081,
"cds_end": null,
"cds_length": 8586,
"cdna_start": 5248,
"cdna_end": null,
"cdna_length": 10866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5081G>C",
"hgvs_p": "p.Arg1694Thr",
"transcript": "ENST00000504915.3",
"protein_id": "ENSP00000473355.2",
"transcript_support_level": 5,
"aa_start": 1694,
"aa_end": null,
"aa_length": 2861,
"cds_start": 5081,
"cds_end": null,
"cds_length": 8586,
"cdna_start": 5137,
"cdna_end": null,
"cdna_length": 9496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5057G>C",
"hgvs_p": "p.Arg1686Thr",
"transcript": "NM_001354897.2",
"protein_id": "NP_001341826.1",
"transcript_support_level": null,
"aa_start": 1686,
"aa_end": null,
"aa_length": 2853,
"cds_start": 5057,
"cds_end": null,
"cds_length": 8562,
"cdna_start": 5277,
"cdna_end": null,
"cdna_length": 10895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "NM_001127510.3",
"protein_id": "NP_001120982.1",
"transcript_support_level": null,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
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"cds_length": 8532,
"cdna_start": 5194,
"cdna_end": null,
"cdna_length": 10812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "NM_001354895.2",
"protein_id": "NP_001341824.1",
"transcript_support_level": null,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5430,
"cdna_end": null,
"cdna_length": 11048,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "NM_001407450.1",
"protein_id": "NP_001394379.1",
"transcript_support_level": null,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
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"cdna_start": 5197,
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"cdna_length": 10815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "ENST00000509732.6",
"protein_id": "ENSP00000426541.2",
"transcript_support_level": 4,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5177,
"cdna_end": null,
"cdna_length": 10616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr",
"transcript": "ENST00000512211.7",
"protein_id": "ENSP00000423828.3",
"transcript_support_level": 2,
"aa_start": 1676,
"aa_end": null,
"aa_length": 2843,
"cds_start": 5027,
"cds_end": null,
"cds_length": 8532,
"cdna_start": 5378,
"cdna_end": null,
"cdna_length": 9737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.5006G>C",
"hgvs_p": "p.Arg1669Thr",
"transcript": "NM_001407451.1",
"protein_id": "NP_001394380.1",
"transcript_support_level": null,
"aa_start": 1669,
"aa_end": null,
"aa_length": 2836,
"cds_start": 5006,
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"cdna_start": 5095,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.4997G>C",
"hgvs_p": "p.Arg1666Thr",
"transcript": "NM_001407452.1",
"protein_id": "NP_001394381.1",
"transcript_support_level": null,
"aa_start": 1666,
"aa_end": null,
"aa_length": 2833,
"cds_start": 4997,
"cds_end": null,
"cds_length": 8502,
"cdna_start": 5400,
"cdna_end": null,
"cdna_length": 11018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.4973G>C",
"hgvs_p": "p.Arg1658Thr",
"transcript": "NM_001127511.3",
"protein_id": "NP_001120983.2",
"transcript_support_level": null,
"aa_start": 1658,
"aa_end": null,
"aa_length": 2825,
"cds_start": 4973,
"cds_end": null,
"cds_length": 8478,
"cdna_start": 5193,
"cdna_end": null,
"cdna_length": 10811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"hgvs_c": "c.4973G>C",
"hgvs_p": "p.Arg1658Thr",
"transcript": "ENST00000507379.6",
"protein_id": "ENSP00000423224.2",
"transcript_support_level": 2,
"aa_start": 1658,
"aa_end": null,
"aa_length": 2825,
"cds_start": 4973,
"cds_end": null,
"cds_length": 8478,
"cdna_start": 5169,
"cdna_end": null,
"cdna_length": 8674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
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{
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}
],
"gene_symbol": "APC",
"gene_hgnc_id": 583,
"dbsnp": "rs143674116",
"frequency_reference_population": 0.000055144894,
"hom_count_reference_population": 0,
"allele_count_reference_population": 89,
"gnomad_exomes_af": 0.0000301014,
"gnomad_genomes_af": 0.00029566,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 45,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03645375370979309,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.239,
"revel_prediction": "Benign",
"alphamissense_score": 0.0904,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.985,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000257430.9",
"gene_symbol": "APC",
"hgnc_id": 583,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.5027G>C",
"hgvs_p": "p.Arg1676Thr"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000520401.1",
"gene_symbol": "ENSG00000258864",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.228+11649G>C",
"hgvs_p": null
}
],
"clinvar_disease": "APC-related disorder,Classic or attenuated familial adenomatous polyposis,Familial adenomatous polyposis 1,Hereditary cancer-predisposing syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:2",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|not provided|not specified|Classic or attenuated familial adenomatous polyposis|Familial adenomatous polyposis 1|APC-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}