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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: 11-119158662-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=119158662&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ABCG4",
"hgnc_id": 13884,
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_022169.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 52,
"alphamissense_prediction": null,
"alphamissense_score": 0.7962,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.910078763961792,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3812,
"cdna_start": 1597,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_022169.5",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000619701.5",
"protein_coding": true,
"protein_id": "NP_071452.2",
"strand": true,
"transcript": "NM_022169.5",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3812,
"cdna_start": 1597,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000619701.5",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_022169.5",
"protein_coding": true,
"protein_id": "ENSP00000481728.1",
"strand": true,
"transcript": "ENST00000619701.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2553,
"cdna_start": 1343,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000622721.1",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000484289.1",
"strand": true,
"transcript": "ENST00000622721.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2719,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000533694.5",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "n.2410G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000533694.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3613,
"cdna_start": 1385,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001142505.1",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135977.1",
"strand": true,
"transcript": "NM_001142505.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3729,
"cdna_start": 1514,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001348191.2",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335120.1",
"strand": true,
"transcript": "NM_001348191.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 646,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2459,
"cdna_start": 1461,
"cds_end": null,
"cds_length": 1941,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000615496.4",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479253.1",
"strand": true,
"transcript": "ENST00000615496.4",
"transcript_support_level": 2
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 593,
"aa_ref": "G",
"aa_start": 425,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3450,
"cdna_start": 1396,
"cds_end": null,
"cds_length": 1782,
"cds_start": 1273,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000912114.1",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1273G>A",
"hgvs_p": "p.Gly425Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582173.1",
"strand": true,
"transcript": "ENST00000912114.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 585,
"aa_ref": "G",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3784,
"cdna_start": 1569,
"cds_end": null,
"cds_length": 1758,
"cds_start": 1090,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001348192.2",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1090G>A",
"hgvs_p": "p.Gly364Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001335121.1",
"strand": true,
"transcript": "NM_001348192.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 582,
"aa_ref": "G",
"aa_start": 361,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3865,
"cdna_start": 1637,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1081,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011542952.3",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1081G>A",
"hgvs_p": "p.Gly361Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011541254.1",
"strand": true,
"transcript": "XM_011542952.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 556,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3296,
"cdna_start": null,
"cds_end": null,
"cds_length": 1671,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000912115.1",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "c.1167+330G>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582174.1",
"strand": true,
"transcript": "ENST00000912115.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1454,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000534402.2",
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"hgvs_c": "n.*167G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000534402.2",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs368538395",
"effect": "missense_variant",
"frequency_reference_population": 0.00003221861,
"gene_hgnc_id": 13884,
"gene_symbol": "ABCG4",
"gnomad_exomes_ac": 51,
"gnomad_exomes_af": 0.0000348885,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657142,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.994,
"pos": 119158662,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.781,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_022169.5"
}
]
}