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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: 2-215015554-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=215015554&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 215015554,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_173076.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "c.1892G>A",
"hgvs_p": "p.Arg631Gln",
"transcript": "NM_173076.3",
"protein_id": "NP_775099.2",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 2595,
"cds_start": 1892,
"cds_end": null,
"cds_length": 7788,
"cdna_start": 2310,
"cdna_end": null,
"cdna_length": 9298,
"mane_select": "ENST00000272895.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "c.1892G>A",
"hgvs_p": "p.Arg631Gln",
"transcript": "ENST00000272895.12",
"protein_id": "ENSP00000272895.7",
"transcript_support_level": 1,
"aa_start": 631,
"aa_end": null,
"aa_length": 2595,
"cds_start": 1892,
"cds_end": null,
"cds_length": 7788,
"cdna_start": 2310,
"cdna_end": null,
"cdna_length": 9298,
"mane_select": "NM_173076.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "c.938G>A",
"hgvs_p": "p.Arg313Gln",
"transcript": "ENST00000389661.4",
"protein_id": "ENSP00000374312.4",
"transcript_support_level": 1,
"aa_start": 313,
"aa_end": null,
"aa_length": 2277,
"cds_start": 938,
"cds_end": null,
"cds_length": 6834,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 7005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "c.938G>A",
"hgvs_p": "p.Arg313Gln",
"transcript": "NM_015657.4",
"protein_id": "NP_056472.2",
"transcript_support_level": null,
"aa_start": 313,
"aa_end": null,
"aa_length": 2277,
"cds_start": 938,
"cds_end": null,
"cds_length": 6834,
"cdna_start": 1097,
"cdna_end": null,
"cdna_length": 8085,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "c.1892G>A",
"hgvs_p": "p.Arg631Gln",
"transcript": "XM_011510951.3",
"protein_id": "XP_011509253.1",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 2598,
"cds_start": 1892,
"cds_end": null,
"cds_length": 7797,
"cdna_start": 2310,
"cdna_end": null,
"cdna_length": 9307,
"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": 16,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"hgvs_c": "n.2334G>A",
"hgvs_p": null,
"transcript": "NR_103740.2",
"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": 9378,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000227769",
"gene_hgnc_id": null,
"hgvs_c": "n.191-2108C>T",
"hgvs_p": null,
"transcript": "ENST00000617699.1",
"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": 351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000227769",
"gene_hgnc_id": null,
"hgvs_c": "n.73+2337C>T",
"hgvs_p": null,
"transcript": "ENST00000627811.1",
"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": 99,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCA12",
"gene_hgnc_id": 14637,
"dbsnp": "rs76979001",
"frequency_reference_population": 0.0018320647,
"hom_count_reference_population": 45,
"allele_count_reference_population": 2957,
"gnomad_exomes_af": 0.00173758,
"gnomad_genomes_af": 0.00273938,
"gnomad_exomes_ac": 2540,
"gnomad_genomes_ac": 417,
"gnomad_exomes_homalt": 42,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003278404474258423,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.144,
"revel_prediction": "Benign",
"alphamissense_score": 0.0789,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.519,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_173076.3",
"gene_symbol": "ABCA12",
"hgnc_id": 14637,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1892G>A",
"hgvs_p": "p.Arg631Gln"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000617699.1",
"gene_symbol": "ENSG00000227769",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.191-2108C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Congenital ichthyosis of skin,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not specified|Congenital ichthyosis of skin|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}