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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: 3-15455920-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=15455920&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 15455920,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000603808.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1174G>A",
"hgvs_p": "p.Asp392Asn",
"transcript": "NM_005677.4",
"protein_id": "NP_005668.2",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 455,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 2960,
"mane_select": "ENST00000383788.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1174G>A",
"hgvs_p": "p.Asp392Asn",
"transcript": "ENST00000383788.10",
"protein_id": "ENSP00000373298.3",
"transcript_support_level": 1,
"aa_start": 392,
"aa_end": null,
"aa_length": 455,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1368,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 2960,
"mane_select": "NM_005677.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1174G>A",
"hgvs_p": "p.Asp392Asn",
"transcript": "ENST00000603808.5",
"protein_id": "ENSP00000474271.1",
"transcript_support_level": 1,
"aa_start": 392,
"aa_end": null,
"aa_length": 456,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 1300,
"cdna_end": null,
"cdna_length": 1668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000293553",
"gene_hgnc_id": null,
"hgvs_c": "n.21G>A",
"hgvs_p": null,
"transcript": "ENST00000629729.3",
"protein_id": "ENSP00000518887.1",
"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": 809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Asp382Asn",
"transcript": "NM_080538.2",
"protein_id": "NP_536799.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 445,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1429,
"cdna_end": null,
"cdna_length": 3134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Asp382Asn",
"transcript": "ENST00000383781.8",
"protein_id": "ENSP00000373291.3",
"transcript_support_level": 5,
"aa_start": 382,
"aa_end": null,
"aa_length": 445,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1429,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1072G>A",
"hgvs_p": "p.Asp358Asn",
"transcript": "NM_080539.4",
"protein_id": "NP_536800.2",
"transcript_support_level": null,
"aa_start": 358,
"aa_end": null,
"aa_length": 421,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "c.1072G>A",
"hgvs_p": "p.Asp358Asn",
"transcript": "ENST00000383786.9",
"protein_id": "ENSP00000373296.3",
"transcript_support_level": 5,
"aa_start": 358,
"aa_end": null,
"aa_length": 421,
"cds_start": 1072,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 1183,
"cdna_end": null,
"cdna_length": 1482,
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.1030G>A",
"hgvs_p": null,
"transcript": "ENST00000604401.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 1771,
"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": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.*936G>A",
"hgvs_p": null,
"transcript": "ENST00000679838.1",
"protein_id": "ENSP00000505708.1",
"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": 2947,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.1086G>A",
"hgvs_p": null,
"transcript": "ENST00000680240.1",
"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": 1682,
"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": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.940G>A",
"hgvs_p": null,
"transcript": "ENST00000680545.1",
"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": 2605,
"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": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.*188G>A",
"hgvs_p": null,
"transcript": "ENST00000681097.1",
"protein_id": "ENSP00000505397.1",
"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": 2783,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.4665G>A",
"hgvs_p": null,
"transcript": "ENST00000681222.1",
"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": 6346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.*936G>A",
"hgvs_p": null,
"transcript": "ENST00000679838.1",
"protein_id": "ENSP00000505708.1",
"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": 2947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"hgvs_c": "n.*188G>A",
"hgvs_p": null,
"transcript": "ENST00000681097.1",
"protein_id": "ENSP00000505397.1",
"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": 2783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COLQ",
"gene_hgnc_id": 2226,
"dbsnp": "rs749266800",
"frequency_reference_population": 0.000017967202,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000157335,
"gnomad_genomes_af": 0.0000394203,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09076899290084839,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1899999976158142,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.173,
"revel_prediction": "Benign",
"alphamissense_score": 0.0704,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.105,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.19,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000603808.5",
"gene_symbol": "COLQ",
"hgnc_id": 2226,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1174G>A",
"hgvs_p": "p.Asp392Asn"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000629729.3",
"gene_symbol": "ENSG00000293553",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.21G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital myasthenic syndrome 5",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Congenital myasthenic syndrome 5",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}