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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: 18-59466820-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=59466820&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 59466820,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000439986.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "NM_133459.4",
"protein_id": "NP_597716.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 406,
"cds_start": 472,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 6271,
"mane_select": "ENST00000439986.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "ENST00000439986.9",
"protein_id": "ENSP00000404464.2",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 406,
"cds_start": 472,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 6271,
"mane_select": "NM_133459.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "ENST00000695904.1",
"protein_id": "ENSP00000512259.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 435,
"cds_start": 472,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 532,
"cdna_end": null,
"cdna_length": 3290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "ENST00000649564.1",
"protein_id": "ENSP00000497183.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 406,
"cds_start": 472,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 685,
"cdna_end": null,
"cdna_length": 6403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "ENST00000650467.2",
"protein_id": "ENSP00000496897.2",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 332,
"cds_start": 472,
"cds_end": null,
"cds_length": 999,
"cdna_start": 569,
"cdna_end": null,
"cdna_length": 6065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "XM_017025557.2",
"protein_id": "XP_016881046.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 435,
"cds_start": 472,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 6575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "XM_047437301.1",
"protein_id": "XP_047293257.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 435,
"cds_start": 472,
"cds_end": null,
"cds_length": 1308,
"cdna_start": 779,
"cdna_end": null,
"cdna_length": 6610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "XM_024451091.2",
"protein_id": "XP_024306859.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 406,
"cds_start": 472,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 744,
"cdna_end": null,
"cdna_length": 6462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "XM_047437302.1",
"protein_id": "XP_047293258.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 406,
"cds_start": 472,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 779,
"cdna_end": null,
"cdna_length": 6497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys",
"transcript": "XM_017025558.2",
"protein_id": "XP_016881047.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 366,
"cds_start": 472,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 553,
"cdna_end": null,
"cdna_length": 6341,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "n.475C>T",
"hgvs_p": null,
"transcript": "ENST00000589419.2",
"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": 1944,
"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": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"hgvs_c": "n.472C>T",
"hgvs_p": null,
"transcript": "ENST00000695903.1",
"protein_id": "ENSP00000512255.1",
"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": 3341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CCBE1",
"gene_hgnc_id": 29426,
"dbsnp": "rs121908253",
"frequency_reference_population": 0.0002132109,
"hom_count_reference_population": 0,
"allele_count_reference_population": 344,
"gnomad_exomes_af": 0.000212843,
"gnomad_genomes_af": 0.000216737,
"gnomad_exomes_ac": 311,
"gnomad_genomes_ac": 33,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4114769995212555,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.752,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2493,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.662,
"phylop100way_prediction": "Benign",
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP5,BP4,BS1_Supporting",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 2,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000439986.9",
"gene_symbol": "CCBE1",
"hgnc_id": 29426,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.472C>T",
"hgvs_p": "p.Arg158Cys"
}
],
"clinvar_disease": "CCBE1-related disorder,Hennekam lymphangiectasia-lymphedema syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:4 US:4 O:1",
"phenotype_combined": "Hennekam lymphangiectasia-lymphedema syndrome 1|not provided|not specified|CCBE1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}