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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: 3-48570304-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=48570304&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 48570304,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000681320.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 98,
"exon_rank_end": null,
"exon_count": 119,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7411C>T",
"hgvs_p": "p.Arg2471*",
"transcript": "NM_000094.4",
"protein_id": "NP_000085.1",
"transcript_support_level": null,
"aa_start": 2471,
"aa_end": null,
"aa_length": 2944,
"cds_start": 7411,
"cds_end": null,
"cds_length": 8835,
"cdna_start": 7474,
"cdna_end": null,
"cdna_length": 9231,
"mane_select": "ENST00000681320.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 98,
"exon_rank_end": null,
"exon_count": 119,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7411C>T",
"hgvs_p": "p.Arg2471*",
"transcript": "ENST00000681320.1",
"protein_id": "ENSP00000506558.1",
"transcript_support_level": null,
"aa_start": 2471,
"aa_end": null,
"aa_length": 2944,
"cds_start": 7411,
"cds_end": null,
"cds_length": 8835,
"cdna_start": 7474,
"cdna_end": null,
"cdna_length": 9231,
"mane_select": "NM_000094.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 97,
"exon_rank_end": null,
"exon_count": 118,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7411C>T",
"hgvs_p": "p.Arg2471*",
"transcript": "ENST00000328333.12",
"protein_id": "ENSP00000332371.8",
"transcript_support_level": 1,
"aa_start": 2471,
"aa_end": null,
"aa_length": 2944,
"cds_start": 7411,
"cds_end": null,
"cds_length": 8835,
"cdna_start": 7519,
"cdna_end": null,
"cdna_length": 9276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.406C>T",
"hgvs_p": "p.Arg136*",
"transcript": "ENST00000422991.1",
"protein_id": "ENSP00000391608.1",
"transcript_support_level": 5,
"aa_start": 136,
"aa_end": null,
"aa_length": 172,
"cds_start": 406,
"cds_end": null,
"cds_length": 519,
"cdna_start": 484,
"cdna_end": null,
"cdna_length": 597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 98,
"exon_rank_end": null,
"exon_count": 106,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7411C>T",
"hgvs_p": "p.Arg2471*",
"transcript": "XM_017005689.2",
"protein_id": "XP_016861178.1",
"transcript_support_level": null,
"aa_start": 2471,
"aa_end": null,
"aa_length": 2609,
"cds_start": 7411,
"cds_end": null,
"cds_length": 7830,
"cdna_start": 7474,
"cdna_end": null,
"cdna_length": 7950,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.138C>T",
"hgvs_p": null,
"transcript": "ENST00000459756.5",
"protein_id": null,
"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": 818,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.161C>T",
"hgvs_p": null,
"transcript": "ENST00000467985.1",
"protein_id": null,
"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": 709,
"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": 62,
"exon_rank_end": null,
"exon_count": 83,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.4050C>T",
"hgvs_p": null,
"transcript": "ENST00000487017.5",
"protein_id": null,
"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": 5807,
"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": 98,
"exon_rank_end": null,
"exon_count": 118,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.7474C>T",
"hgvs_p": null,
"transcript": "XR_001740003.2",
"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": 8849,
"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": 98,
"exon_rank_end": null,
"exon_count": 118,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.7474C>T",
"hgvs_p": null,
"transcript": "XR_001740004.2",
"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": 8813,
"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": 98,
"exon_rank_end": null,
"exon_count": 118,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.7474C>T",
"hgvs_p": null,
"transcript": "XR_001740005.2",
"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": 8810,
"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": 98,
"exon_rank_end": null,
"exon_count": 101,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "n.7448C>T",
"hgvs_p": null,
"transcript": "XR_001740006.2",
"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": 7568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 118,
"intron_rank": 97,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7381-126C>T",
"hgvs_p": null,
"transcript": "XM_017005688.2",
"protein_id": "XP_016861177.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2924,
"cds_start": -4,
"cds_end": null,
"cds_length": 8775,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9171,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": 97,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7381-52C>T",
"hgvs_p": null,
"transcript": "XM_017005690.2",
"protein_id": "XP_016861179.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2470,
"cds_start": -4,
"cds_end": null,
"cds_length": 7413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 98,
"intron_rank": 97,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7355-52C>T",
"hgvs_p": null,
"transcript": "XM_017005691.2",
"protein_id": "XP_016861180.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2466,
"cds_start": -4,
"cds_end": null,
"cds_length": 7401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 99,
"intron_rank": 97,
"intron_rank_end": null,
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"hgvs_c": "c.7355-126C>T",
"hgvs_p": null,
"transcript": "XM_017005692.2",
"protein_id": "XP_016861181.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2452,
"cds_start": -4,
"cds_end": null,
"cds_length": 7359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7498,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL7A1",
"gene_hgnc_id": 2214,
"dbsnp": "rs121912852",
"frequency_reference_population": 0.000002052183,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205218,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5099999904632568,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.51,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.944,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000681320.1",
"gene_symbol": "COL7A1",
"hgnc_id": 2214,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.7411C>T",
"hgvs_p": "p.Arg2471*"
}
],
"clinvar_disease": "7 conditions,Epidermolysis bullosa dystrophica,Recessive dystrophic epidermolysis bullosa,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Recessive dystrophic epidermolysis bullosa|not provided|7 conditions|Epidermolysis bullosa dystrophica",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}