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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: 10-63214623-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=63214623&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 63214623,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000399262.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.1544A>G",
"hgvs_p": "p.Asp515Gly",
"transcript": "NM_032776.3",
"protein_id": "NP_116165.1",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 2540,
"cds_start": 1544,
"cds_end": null,
"cds_length": 7623,
"cdna_start": 1859,
"cdna_end": null,
"cdna_length": 8758,
"mane_select": "ENST00000399262.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.1544A>G",
"hgvs_p": "p.Asp515Gly",
"transcript": "ENST00000399262.7",
"protein_id": "ENSP00000382204.2",
"transcript_support_level": 5,
"aa_start": 515,
"aa_end": null,
"aa_length": 2540,
"cds_start": 1544,
"cds_end": null,
"cds_length": 7623,
"cdna_start": 1859,
"cdna_end": null,
"cdna_length": 8758,
"mane_select": "NM_032776.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "ENST00000542921.5",
"protein_id": "ENSP00000444682.1",
"transcript_support_level": 1,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 8149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "n.1516A>G",
"hgvs_p": null,
"transcript": "ENST00000402544.5",
"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": 8011,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.1430A>G",
"hgvs_p": "p.Asp477Gly",
"transcript": "NM_001322252.2",
"protein_id": "NP_001309181.1",
"transcript_support_level": null,
"aa_start": 477,
"aa_end": null,
"aa_length": 2502,
"cds_start": 1430,
"cds_end": null,
"cds_length": 7509,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 8644,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "NM_001282948.2",
"protein_id": "NP_001269877.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1792,
"cdna_end": null,
"cdna_length": 8691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "NM_001318154.2",
"protein_id": "NP_001305083.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1529,
"cdna_end": null,
"cdna_length": 8428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.887A>G",
"hgvs_p": "p.Asp296Gly",
"transcript": "NM_001322254.2",
"protein_id": "NP_001309183.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 2321,
"cds_start": 887,
"cds_end": null,
"cds_length": 6966,
"cdna_start": 1686,
"cdna_end": null,
"cdna_length": 8585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.887A>G",
"hgvs_p": "p.Asp296Gly",
"transcript": "NM_001322258.2",
"protein_id": "NP_001309187.1",
"transcript_support_level": null,
"aa_start": 296,
"aa_end": null,
"aa_length": 2321,
"cds_start": 887,
"cds_end": null,
"cds_length": 6966,
"cdna_start": 1423,
"cdna_end": null,
"cdna_length": 8322,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.680A>G",
"hgvs_p": "p.Asp227Gly",
"transcript": "NM_001318153.2",
"protein_id": "NP_001305082.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 2252,
"cds_start": 680,
"cds_end": null,
"cds_length": 6759,
"cdna_start": 1796,
"cdna_end": null,
"cdna_length": 8695,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.1382A>G",
"hgvs_p": "p.Asp461Gly",
"transcript": "XM_047424774.1",
"protein_id": "XP_047280730.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 2486,
"cds_start": 1382,
"cds_end": null,
"cds_length": 7461,
"cdna_start": 5230,
"cdna_end": null,
"cdna_length": 12129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_017015897.2",
"protein_id": "XP_016871386.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1415,
"cdna_end": null,
"cdna_length": 8314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_017015898.2",
"protein_id": "XP_016871387.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 14844,
"cdna_end": null,
"cdna_length": 21743,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_047424772.1",
"protein_id": "XP_047280728.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1595,
"cdna_end": null,
"cdna_length": 8494,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_047424773.1",
"protein_id": "XP_047280729.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 2358,
"cds_start": 998,
"cds_end": null,
"cds_length": 7077,
"cdna_start": 1481,
"cdna_end": null,
"cdna_length": 8380,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_047424775.1",
"protein_id": "XP_047280731.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 1850,
"cds_start": 998,
"cds_end": null,
"cds_length": 5553,
"cdna_start": 1595,
"cdna_end": null,
"cdna_length": 6163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "c.998A>G",
"hgvs_p": "p.Asp333Gly",
"transcript": "XM_011539508.3",
"protein_id": "XP_011537810.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 1518,
"cds_start": 998,
"cds_end": null,
"cds_length": 4557,
"cdna_start": 1595,
"cdna_end": null,
"cdna_length": 7323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "JMJD1C",
"gene_hgnc_id": 12313,
"hgvs_c": "n.1572A>G",
"hgvs_p": null,
"transcript": "NR_134512.2",
"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": 8190,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "JMJD1C",
"gene_hgnc_id": 12313,
"dbsnp": "rs61758117",
"frequency_reference_population": 0.00011647011,
"hom_count_reference_population": 0,
"allele_count_reference_population": 188,
"gnomad_exomes_af": 0.0000595153,
"gnomad_genomes_af": 0.000662999,
"gnomad_exomes_ac": 87,
"gnomad_genomes_ac": 101,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.005157977342605591,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.099,
"revel_prediction": "Benign",
"alphamissense_score": 0.1013,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.389,
"phylop100way_prediction": "Uncertain_significance",
"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_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000399262.7",
"gene_symbol": "JMJD1C",
"hgnc_id": 12313,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1544A>G",
"hgvs_p": "p.Asp515Gly"
}
],
"clinvar_disease": "Early myoclonic encephalopathy,JMJD1C-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Early myoclonic encephalopathy|JMJD1C-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}