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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: 2-189010657-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189010657&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 189010657,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000090.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.4021G>A",
"hgvs_p": "p.Gly1341Ser",
"transcript": "NM_000090.4",
"protein_id": "NP_000081.2",
"transcript_support_level": null,
"aa_start": 1341,
"aa_end": null,
"aa_length": 1466,
"cds_start": 4021,
"cds_end": null,
"cds_length": 4401,
"cdna_start": 4138,
"cdna_end": null,
"cdna_length": 5490,
"mane_select": "ENST00000304636.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000090.4"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.4021G>A",
"hgvs_p": "p.Gly1341Ser",
"transcript": "ENST00000304636.9",
"protein_id": "ENSP00000304408.4",
"transcript_support_level": 1,
"aa_start": 1341,
"aa_end": null,
"aa_length": 1466,
"cds_start": 4021,
"cds_end": null,
"cds_length": 4401,
"cdna_start": 4138,
"cdna_end": null,
"cdna_length": 5490,
"mane_select": "NM_000090.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304636.9"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3922G>A",
"hgvs_p": "p.Gly1308Ser",
"transcript": "ENST00000450867.2",
"protein_id": "ENSP00000415346.2",
"transcript_support_level": 1,
"aa_start": 1308,
"aa_end": null,
"aa_length": 1433,
"cds_start": 3922,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4039,
"cdna_end": null,
"cdna_length": 5391,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450867.2"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.4012G>A",
"hgvs_p": "p.Gly1338Ser",
"transcript": "ENST00000879201.1",
"protein_id": "ENSP00000549260.1",
"transcript_support_level": null,
"aa_start": 1338,
"aa_end": null,
"aa_length": 1463,
"cds_start": 4012,
"cds_end": null,
"cds_length": 4392,
"cdna_start": 4129,
"cdna_end": null,
"cdna_length": 4787,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879201.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3976G>A",
"hgvs_p": "p.Gly1326Ser",
"transcript": "ENST00000879198.1",
"protein_id": "ENSP00000549257.1",
"transcript_support_level": null,
"aa_start": 1326,
"aa_end": null,
"aa_length": 1451,
"cds_start": 3976,
"cds_end": null,
"cds_length": 4356,
"cdna_start": 4093,
"cdna_end": null,
"cdna_length": 4757,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879198.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3970G>A",
"hgvs_p": "p.Gly1324Ser",
"transcript": "ENST00000879194.1",
"protein_id": "ENSP00000549253.1",
"transcript_support_level": null,
"aa_start": 1324,
"aa_end": null,
"aa_length": 1449,
"cds_start": 3970,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 4087,
"cdna_end": null,
"cdna_length": 5436,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879194.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3967G>A",
"hgvs_p": "p.Gly1323Ser",
"transcript": "ENST00000879200.1",
"protein_id": "ENSP00000549259.1",
"transcript_support_level": null,
"aa_start": 1323,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3967,
"cds_end": null,
"cds_length": 4347,
"cdna_start": 4084,
"cdna_end": null,
"cdna_length": 4742,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879200.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3967G>A",
"hgvs_p": "p.Gly1323Ser",
"transcript": "ENST00000879202.1",
"protein_id": "ENSP00000549261.1",
"transcript_support_level": null,
"aa_start": 1323,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3967,
"cds_end": null,
"cds_length": 4347,
"cdna_start": 4084,
"cdna_end": null,
"cdna_length": 4669,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879202.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3967G>A",
"hgvs_p": "p.Gly1323Ser",
"transcript": "ENST00000957918.1",
"protein_id": "ENSP00000627977.1",
"transcript_support_level": null,
"aa_start": 1323,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3967,
"cds_end": null,
"cds_length": 4347,
"cdna_start": 4084,
"cdna_end": null,
"cdna_length": 4743,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957918.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3922G>A",
"hgvs_p": "p.Gly1308Ser",
"transcript": "ENST00000879195.1",
"protein_id": "ENSP00000549254.1",
"transcript_support_level": null,
"aa_start": 1308,
"aa_end": null,
"aa_length": 1433,
"cds_start": 3922,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4039,
"cdna_end": null,
"cdna_length": 5388,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879195.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3913G>A",
"hgvs_p": "p.Gly1305Ser",
"transcript": "ENST00000879196.1",
"protein_id": "ENSP00000549255.1",
"transcript_support_level": null,
"aa_start": 1305,
"aa_end": null,
"aa_length": 1430,
"cds_start": 3913,
"cds_end": null,
"cds_length": 4293,
"cdna_start": 4030,
"cdna_end": null,
"cdna_length": 5376,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879196.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3913G>A",
"hgvs_p": "p.Gly1305Ser",
"transcript": "ENST00000879197.1",
"protein_id": "ENSP00000549256.1",
"transcript_support_level": null,
"aa_start": 1305,
"aa_end": null,
"aa_length": 1430,
"cds_start": 3913,
"cds_end": null,
"cds_length": 4293,
"cdna_start": 3999,
"cdna_end": null,
"cdna_length": 5349,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879197.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3913G>A",
"hgvs_p": "p.Gly1305Ser",
"transcript": "ENST00000957916.1",
"protein_id": "ENSP00000627975.1",
"transcript_support_level": null,
"aa_start": 1305,
"aa_end": null,
"aa_length": 1430,
"cds_start": 3913,
"cds_end": null,
"cds_length": 4293,
"cdna_start": 4030,
"cdna_end": null,
"cdna_length": 5382,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957916.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3901G>A",
"hgvs_p": "p.Gly1301Ser",
"transcript": "ENST00000957917.1",
"protein_id": "ENSP00000627976.1",
"transcript_support_level": null,
"aa_start": 1301,
"aa_end": null,
"aa_length": 1426,
"cds_start": 3901,
"cds_end": null,
"cds_length": 4281,
"cdna_start": 4020,
"cdna_end": null,
"cdna_length": 5369,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957917.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 49,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3898G>A",
"hgvs_p": "p.Gly1300Ser",
"transcript": "ENST00000879203.1",
"protein_id": "ENSP00000549262.1",
"transcript_support_level": null,
"aa_start": 1300,
"aa_end": null,
"aa_length": 1425,
"cds_start": 3898,
"cds_end": null,
"cds_length": 4278,
"cdna_start": 4015,
"cdna_end": null,
"cdna_length": 4428,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879203.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3877G>A",
"hgvs_p": "p.Gly1293Ser",
"transcript": "ENST00000879199.1",
"protein_id": "ENSP00000549258.1",
"transcript_support_level": null,
"aa_start": 1293,
"aa_end": null,
"aa_length": 1418,
"cds_start": 3877,
"cds_end": null,
"cds_length": 4257,
"cdna_start": 3994,
"cdna_end": null,
"cdna_length": 4655,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879199.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3868G>A",
"hgvs_p": "p.Gly1290Ser",
"transcript": "ENST00000713745.1",
"protein_id": "ENSP00000519049.1",
"transcript_support_level": null,
"aa_start": 1290,
"aa_end": null,
"aa_length": 1415,
"cds_start": 3868,
"cds_end": null,
"cds_length": 4248,
"cdna_start": 3985,
"cdna_end": null,
"cdna_length": 5337,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713745.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 48,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "c.3859G>A",
"hgvs_p": "p.Gly1287Ser",
"transcript": "ENST00000713744.1",
"protein_id": "ENSP00000519048.1",
"transcript_support_level": null,
"aa_start": 1287,
"aa_end": null,
"aa_length": 1412,
"cds_start": 3859,
"cds_end": null,
"cds_length": 4239,
"cdna_start": 3976,
"cdna_end": null,
"cdna_length": 5328,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000713744.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"hgvs_c": "n.1400G>A",
"hgvs_p": null,
"transcript": "ENST00000487010.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2054,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000487010.1"
}
],
"gene_symbol": "COL3A1",
"gene_hgnc_id": 2201,
"dbsnp": "rs140646380",
"frequency_reference_population": 0.000121435165,
"hom_count_reference_population": 0,
"allele_count_reference_population": 196,
"gnomad_exomes_af": 0.00011903,
"gnomad_genomes_af": 0.000144531,
"gnomad_exomes_ac": 174,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04934343695640564,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.501,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1462,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_000090.4",
"gene_symbol": "COL3A1",
"hgnc_id": 2201,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4021G>A",
"hgvs_p": "p.Gly1341Ser"
}
],
"clinvar_disease": " type 4,Ehlers-Danlos syndrome,Familial thoracic aortic aneurysm and aortic dissection,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:6 B:1",
"phenotype_combined": "Ehlers-Danlos syndrome, type 4|not provided|Familial thoracic aortic aneurysm and aortic dissection|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}