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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: 19-10287311-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=10287311&ref=A&alt=G&genome=hg38&allGenes=true"
API Response
json
{
"variants": [
{
"chr": "19",
"pos": 10287311,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000380770.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg",
"transcript": "NM_001544.5",
"protein_id": "NP_001535.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 271,
"cds_start": 299,
"cds_end": null,
"cds_length": 816,
"cdna_start": 357,
"cdna_end": null,
"cdna_length": 1290,
"mane_select": "ENST00000380770.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg",
"transcript": "ENST00000380770.5",
"protein_id": "ENSP00000370147.2",
"transcript_support_level": 1,
"aa_start": 100,
"aa_end": null,
"aa_length": 271,
"cds_start": 299,
"cds_end": null,
"cds_length": 816,
"cdna_start": 357,
"cdna_end": null,
"cdna_length": 1290,
"mane_select": "NM_001544.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg",
"transcript": "ENST00000340992.4",
"protein_id": "ENSP00000342114.3",
"transcript_support_level": 1,
"aa_start": 100,
"aa_end": null,
"aa_length": 272,
"cds_start": 299,
"cds_end": null,
"cds_length": 819,
"cdna_start": 338,
"cdna_end": null,
"cdna_length": 1176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg",
"transcript": "NM_001039132.3",
"protein_id": "NP_001034221.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 272,
"cds_start": 299,
"cds_end": null,
"cds_length": 819,
"cdna_start": 357,
"cdna_end": null,
"cdna_length": 1213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg",
"transcript": "ENST00000393717.2",
"protein_id": "ENSP00000377320.1",
"transcript_support_level": 2,
"aa_start": 100,
"aa_end": null,
"aa_length": 237,
"cds_start": 299,
"cds_end": null,
"cds_length": 714,
"cdna_start": 308,
"cdna_end": null,
"cdna_length": 1390,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4-AS1",
"gene_hgnc_id": 55990,
"hgvs_c": "n.1709T>C",
"hgvs_p": null,
"transcript": "ENST00000589379.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 3219,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ICAM4-AS1",
"gene_hgnc_id": 55990,
"hgvs_c": "n.1709T>C",
"hgvs_p": null,
"transcript": "NR_186335.1",
"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": 3219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LIMASI",
"gene_hgnc_id": 56357,
"hgvs_c": "n.395+3108T>C",
"hgvs_p": null,
"transcript": "ENST00000715961.1",
"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": 919,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ICAM4-AS1",
"gene_hgnc_id": 55990,
"hgvs_c": "n.380-1372T>C",
"hgvs_p": null,
"transcript": "ENST00000724881.1",
"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": 522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ICAM4",
"gene_hgnc_id": 5347,
"dbsnp": "rs77493670",
"frequency_reference_population": 0.0036413437,
"hom_count_reference_population": 61,
"allele_count_reference_population": 5876,
"gnomad_exomes_af": 0.00348709,
"gnomad_genomes_af": 0.00512147,
"gnomad_exomes_ac": 5096,
"gnomad_genomes_ac": 780,
"gnomad_exomes_homalt": 49,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00964897871017456,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.17,
"revel_prediction": "Benign",
"alphamissense_score": 0.1326,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.522,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000380770.5",
"gene_symbol": "ICAM4",
"hgnc_id": 5347,
"effects": [
"missense_variant"
],
"inheritance_mode": "BG",
"hgvs_c": "c.299A>G",
"hgvs_p": "p.Gln100Arg"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NR_186335.1",
"gene_symbol": "ICAM4-AS1",
"hgnc_id": 55990,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1709T>C",
"hgvs_p": null
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000715961.1",
"gene_symbol": "LIMASI",
"hgnc_id": 56357,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.395+3108T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Landsteiner-Wiener phenotype",
"clinvar_classification": "Affects",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Landsteiner-Wiener phenotype",
"pathogenicity_classification_combined": "Affects",
"custom_annotations": null
}
],
"message": null
}