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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: 2-188995091-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=188995091&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 188995091,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000090.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "NM_000090.4",
"protein_id": "NP_000081.2",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1466,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000304636.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000090.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000304636.9",
"protein_id": "ENSP00000304408.4",
"transcript_support_level": 1,
"aa_start": 501,
"aa_end": null,
"aa_length": 1466,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000090.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304636.9"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1402G>A",
"hgvs_p": "p.Gly468Arg",
"transcript": "ENST00000450867.2",
"protein_id": "ENSP00000415346.2",
"transcript_support_level": 1,
"aa_start": 468,
"aa_end": null,
"aa_length": 1433,
"cds_start": 1402,
"cds_end": null,
"cds_length": 4302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450867.2"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1492G>A",
"hgvs_p": "p.Gly498Arg",
"transcript": "ENST00000879201.1",
"protein_id": "ENSP00000549260.1",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 1463,
"cds_start": 1492,
"cds_end": null,
"cds_length": 4392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879201.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1456G>A",
"hgvs_p": "p.Gly486Arg",
"transcript": "ENST00000879198.1",
"protein_id": "ENSP00000549257.1",
"transcript_support_level": null,
"aa_start": 486,
"aa_end": null,
"aa_length": 1451,
"cds_start": 1456,
"cds_end": null,
"cds_length": 4356,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879198.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1450G>A",
"hgvs_p": "p.Gly484Arg",
"transcript": "ENST00000879194.1",
"protein_id": "ENSP00000549253.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 1449,
"cds_start": 1450,
"cds_end": null,
"cds_length": 4350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879194.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000879200.1",
"protein_id": "ENSP00000549259.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1448,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879200.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000879202.1",
"protein_id": "ENSP00000549261.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1448,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879202.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1447G>A",
"hgvs_p": "p.Gly483Arg",
"transcript": "ENST00000957918.1",
"protein_id": "ENSP00000627977.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 1448,
"cds_start": 1447,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957918.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000879195.1",
"protein_id": "ENSP00000549254.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1433,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879195.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1393G>A",
"hgvs_p": "p.Gly465Arg",
"transcript": "ENST00000879196.1",
"protein_id": "ENSP00000549255.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 1430,
"cds_start": 1393,
"cds_end": null,
"cds_length": 4293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879196.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000879197.1",
"protein_id": "ENSP00000549256.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1430,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879197.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000957916.1",
"protein_id": "ENSP00000627975.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1430,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957916.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000957917.1",
"protein_id": "ENSP00000627976.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1426,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4281,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957917.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000879203.1",
"protein_id": "ENSP00000549262.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1425,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879203.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1357G>A",
"hgvs_p": "p.Gly453Arg",
"transcript": "ENST00000879199.1",
"protein_id": "ENSP00000549258.1",
"transcript_support_level": null,
"aa_start": 453,
"aa_end": null,
"aa_length": 1418,
"cds_start": 1357,
"cds_end": null,
"cds_length": 4257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879199.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000713745.1",
"protein_id": "ENSP00000519049.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1415,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713745.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg",
"transcript": "ENST00000713744.1",
"protein_id": "ENSP00000519048.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 1412,
"cds_start": 1501,
"cds_end": null,
"cds_length": 4239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713744.1"
}
],
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"dbsnp": "rs587779523",
"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": 0.9933761358261108,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.951,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9909,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.055,
"phylop100way_prediction": "Pathogenic",
"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": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000090.4",
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1501G>A",
"hgvs_p": "p.Gly501Arg"
}
],
"clinvar_disease": " type 4,Ehlers-Danlos syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}