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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: 17-50186774-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50186774&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"PM1",
"PP2",
"BP4_Moderate",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "COL1A1",
"hgnc_id": 2197,
"hgvs_c": "c.3680G>A",
"hgvs_p": "p.Arg1227His",
"inheritance_mode": "AD",
"pathogenic_score": 3,
"score": -4,
"transcript": "NM_000088.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,PP2,BP4_Moderate,BP6,BS2",
"acmg_score": -4,
"allele_count_reference_population": 49,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.294,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.06,
"chr": "17",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "COL1A1-related disorder,Cardiovascular phenotype,Osteogenesis imperfecta type I,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.20649224519729614,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1464,
"aa_ref": "R",
"aa_start": 1227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5914,
"cdna_start": 3798,
"cds_end": null,
"cds_length": 4395,
"cds_start": 3680,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "NM_000088.4",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3680G>A",
"hgvs_p": "p.Arg1227His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000225964.10",
"protein_coding": true,
"protein_id": "NP_000079.2",
"strand": false,
"transcript": "NM_000088.4",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1464,
"aa_ref": "R",
"aa_start": 1227,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5914,
"cdna_start": 3798,
"cds_end": null,
"cds_length": 4395,
"cds_start": 3680,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000225964.10",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3680G>A",
"hgvs_p": "p.Arg1227His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000088.4",
"protein_coding": true,
"protein_id": "ENSP00000225964.6",
"strand": false,
"transcript": "ENST00000225964.10",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "R",
"aa_start": 1226,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4778,
"cdna_start": 3793,
"cds_end": null,
"cds_length": 4392,
"cds_start": 3677,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000861334.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3677G>A",
"hgvs_p": "p.Arg1226His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531393.1",
"strand": false,
"transcript": "ENST00000861334.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1463,
"aa_ref": "R",
"aa_start": 1227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4765,
"cdna_start": 3798,
"cds_end": null,
"cds_length": 4392,
"cds_start": 3680,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000861339.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3680G>A",
"hgvs_p": "p.Arg1227His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531398.1",
"strand": false,
"transcript": "ENST00000861339.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1459,
"aa_ref": "R",
"aa_start": 1222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4752,
"cdna_start": 3786,
"cds_end": null,
"cds_length": 4380,
"cds_start": 3665,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000861340.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3665G>A",
"hgvs_p": "p.Arg1222His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531399.1",
"strand": false,
"transcript": "ENST00000861340.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1452,
"aa_ref": "R",
"aa_start": 1215,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4732,
"cdna_start": 3762,
"cds_end": null,
"cds_length": 4359,
"cds_start": 3644,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000861338.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3644G>A",
"hgvs_p": "p.Arg1215His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531397.1",
"strand": false,
"transcript": "ENST00000861338.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1446,
"aa_ref": "R",
"aa_start": 1209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4714,
"cdna_start": 3744,
"cds_end": null,
"cds_length": 4341,
"cds_start": 3626,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000861336.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3626G>A",
"hgvs_p": "p.Arg1209His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531395.1",
"strand": false,
"transcript": "ENST00000861336.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1446,
"aa_ref": "R",
"aa_start": 1209,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4710,
"cdna_start": 3744,
"cds_end": null,
"cds_length": 4341,
"cds_start": 3626,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000861342.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3626G>A",
"hgvs_p": "p.Arg1209His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531401.1",
"strand": false,
"transcript": "ENST00000861342.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1431,
"aa_ref": "R",
"aa_start": 1194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4687,
"cdna_start": 3698,
"cds_end": null,
"cds_length": 4296,
"cds_start": 3581,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000919350.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3581G>A",
"hgvs_p": "p.Arg1194His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000589409.1",
"strand": false,
"transcript": "ENST00000919350.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1428,
"aa_ref": "R",
"aa_start": 1191,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4656,
"cdna_start": 3690,
"cds_end": null,
"cds_length": 4287,
"cds_start": 3572,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000861343.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3572G>A",
"hgvs_p": "p.Arg1191His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531402.1",
"strand": false,
"transcript": "ENST00000861343.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1422,
"aa_ref": "R",
"aa_start": 1185,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4642,
"cdna_start": 3672,
"cds_end": null,
"cds_length": 4269,
"cds_start": 3554,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 48,
"exon_rank_end": null,
"feature": "ENST00000861337.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3554G>A",
"hgvs_p": "p.Arg1185His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531396.1",
"strand": false,
"transcript": "ENST00000861337.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1419,
"aa_ref": "R",
"aa_start": 1182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4627,
"cdna_start": 3661,
"cds_end": null,
"cds_length": 4260,
"cds_start": 3545,
"consequences": [
"missense_variant"
],
"exon_count": 50,
"exon_rank": 47,
"exon_rank_end": null,
"feature": "ENST00000861344.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3545G>A",
"hgvs_p": "p.Arg1182His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531403.1",
"strand": false,
"transcript": "ENST00000861344.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 1203,
"aa_ref": "R",
"aa_start": 966,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3981,
"cdna_start": 3015,
"cds_end": null,
"cds_length": 3612,
"cds_start": 2897,
"consequences": [
"missense_variant"
],
"exon_count": 40,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "ENST00000861341.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.2897G>A",
"hgvs_p": "p.Arg966His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531400.1",
"strand": false,
"transcript": "ENST00000861341.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 1071,
"aa_ref": "R",
"aa_start": 834,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3589,
"cdna_start": 2619,
"cds_end": null,
"cds_length": 3216,
"cds_start": 2501,
"consequences": [
"missense_variant"
],
"exon_count": 35,
"exon_rank": 32,
"exon_rank_end": null,
"feature": "ENST00000861335.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.2501G>A",
"hgvs_p": "p.Arg834His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531394.1",
"strand": false,
"transcript": "ENST00000861335.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 930,
"aa_ref": "R",
"aa_start": 693,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3182,
"cdna_start": 2196,
"cds_end": null,
"cds_length": 2793,
"cds_start": 2078,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000861333.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.2078G>A",
"hgvs_p": "p.Arg693His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531392.1",
"strand": false,
"transcript": "ENST00000861333.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 921,
"aa_ref": "R",
"aa_start": 684,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3106,
"cdna_start": 2165,
"cds_end": null,
"cds_length": 2766,
"cds_start": 2051,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000963828.1",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.2051G>A",
"hgvs_p": "p.Arg684His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000633887.1",
"strand": false,
"transcript": "ENST00000963828.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
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"aa_length": 1398,
"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5716,
"cdna_start": 3600,
"cds_end": null,
"cds_length": 4197,
"cds_start": 3482,
"consequences": [
"missense_variant"
],
"exon_count": 48,
"exon_rank": 45,
"exon_rank_end": null,
"feature": "XM_011524341.2",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3482G>A",
"hgvs_p": "p.Arg1161His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011522643.1",
"strand": false,
"transcript": "XM_011524341.2",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
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"cdna_end": null,
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"cdna_start": 3528,
"cds_end": null,
"cds_length": 4125,
"cds_start": 3410,
"consequences": [
"missense_variant"
],
"exon_count": 49,
"exon_rank": 46,
"exon_rank_end": null,
"feature": "XM_005257058.5",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.3410G>A",
"hgvs_p": "p.Arg1137His",
"intron_rank": null,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257115.2",
"strand": false,
"transcript": "XM_005257058.5",
"transcript_support_level": null
},
{
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"aa_ref": "R",
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4996,
"cdna_start": 2880,
"cds_end": null,
"cds_length": 3477,
"cds_start": 2762,
"consequences": [
"missense_variant"
],
"exon_count": 38,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "XM_005257059.5",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "c.2762G>A",
"hgvs_p": "p.Arg921His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257116.2",
"strand": false,
"transcript": "XM_005257059.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1147,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000510710.3",
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"hgvs_c": "n.349G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000510710.3",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs543809032",
"effect": "missense_variant",
"frequency_reference_population": 0.000030358415,
"gene_hgnc_id": 2197,
"gene_symbol": "COL1A1",
"gnomad_exomes_ac": 44,
"gnomad_exomes_af": 0.0000301003,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328364,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Cardiovascular phenotype|Osteogenesis imperfecta type I|not specified|COL1A1-related disorder|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.991,
"pos": 50186774,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.485,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000088.4"
}
]
}