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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: 3-184358227-TGATGAG-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=184358227&ref=TGATGAG&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 184358227,
"ref": "TGATGAG",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000265593.9",
"consequences": [
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "NM_004366.6",
"protein_id": "NP_004357.3",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 898,
"cds_start": 430,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": "ENST00000265593.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "ENST00000265593.9",
"protein_id": "ENSP00000265593.4",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 898,
"cds_start": 430,
"cds_end": null,
"cds_length": 2697,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": "NM_004366.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "ENST00000344937.11",
"protein_id": "ENSP00000345056.7",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 881,
"cds_start": 430,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 3187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "NM_001171087.3",
"protein_id": "NP_001164558.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 881,
"cds_start": 430,
"cds_end": null,
"cds_length": 2646,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 3193,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "NM_001171089.3",
"protein_id": "NP_001164560.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 869,
"cds_start": 430,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 3157,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "ENST00000457512.1",
"protein_id": "ENSP00000391928.1",
"transcript_support_level": 2,
"aa_start": 144,
"aa_end": null,
"aa_length": 869,
"cds_start": 430,
"cds_end": null,
"cds_length": 2610,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 2820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.298_303delCTCATC",
"hgvs_p": "p.Leu100_Ile101del",
"transcript": "NM_001171088.3",
"protein_id": "NP_001164559.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 854,
"cds_start": 298,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 3112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.298_303delCTCATC",
"hgvs_p": "p.Leu100_Ile101del",
"transcript": "ENST00000434054.6",
"protein_id": "ENSP00000400425.2",
"transcript_support_level": 2,
"aa_start": 100,
"aa_end": null,
"aa_length": 854,
"cds_start": 298,
"cds_end": null,
"cds_length": 2565,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 2897,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.313_318delCTCATC",
"hgvs_p": "p.Leu105_Ile106del",
"transcript": "ENST00000636492.1",
"protein_id": "ENSP00000490313.1",
"transcript_support_level": 5,
"aa_start": 105,
"aa_end": null,
"aa_length": 464,
"cds_start": 313,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 318,
"cdna_end": null,
"cdna_length": 1395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "XM_006713489.2",
"protein_id": "XP_006713552.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 863,
"cds_start": 430,
"cds_end": null,
"cds_length": 2592,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 3139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "XM_011512401.2",
"protein_id": "XP_011510703.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 835,
"cds_start": 430,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 6968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "LI",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del",
"transcript": "XM_047447419.1",
"protein_id": "XP_047303375.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 529,
"cds_start": 430,
"cds_end": null,
"cds_length": 1590,
"cdna_start": 561,
"cdna_end": null,
"cdna_length": 1904,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.426_431delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000465231.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cds_length": null,
"cdna_start": null,
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"cdna_length": 601,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.437_442delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000485667.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_length": 1652,
"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": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.430_435delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000636180.1",
"protein_id": "ENSP00000490374.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 3019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.397_402delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000636241.1",
"protein_id": "ENSP00000490299.1",
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.430_435delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000636661.1",
"protein_id": "ENSP00000490764.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 4378,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.406_411delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000637392.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cdna_length": 4615,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.136_141delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000637909.1",
"protein_id": "ENSP00000490570.1",
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"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.394_399delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000638134.1",
"protein_id": "ENSP00000490659.1",
"transcript_support_level": 5,
"aa_start": null,
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"aa_length": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"hgvs_c": "n.-185_-180delCTCATC",
"hgvs_p": null,
"transcript": "ENST00000475279.2",
"protein_id": "ENSP00000489885.1",
"transcript_support_level": 5,
"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": 938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLCN2",
"gene_hgnc_id": 2020,
"dbsnp": "rs587777110",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.31,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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_pathogenic",
"acmg_criteria": "PM2,PM4,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM4",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000265593.9",
"gene_symbol": "CLCN2",
"hgnc_id": 2020,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.430_435delCTCATC",
"hgvs_p": "p.Leu144_Ile145del"
}
],
"clinvar_disease": "Leukoencephalopathy with mild cerebellar ataxia and white matter edema",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Leukoencephalopathy with mild cerebellar ataxia and white matter edema",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}