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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: 16-176765-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=176765&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 176765,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000320868.9",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"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": "HBA1",
"gene_hgnc_id": 4823,
"hgvs_c": "c.49A>G",
"hgvs_p": "p.Lys17Glu",
"transcript": "NM_000558.5",
"protein_id": "NP_000549.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 142,
"cds_start": 49,
"cds_end": null,
"cds_length": 429,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 577,
"mane_select": "ENST00000320868.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"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": "HBA1",
"gene_hgnc_id": 4823,
"hgvs_c": "c.49A>G",
"hgvs_p": "p.Lys17Glu",
"transcript": "ENST00000320868.9",
"protein_id": "ENSP00000322421.5",
"transcript_support_level": 1,
"aa_start": 17,
"aa_end": null,
"aa_length": 142,
"cds_start": 49,
"cds_end": null,
"cds_length": 429,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 577,
"mane_select": "NM_000558.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA1",
"gene_hgnc_id": 4823,
"hgvs_c": "n.68A>G",
"hgvs_p": null,
"transcript": "ENST00000472694.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA1",
"gene_hgnc_id": 4823,
"hgvs_c": "n.18A>G",
"hgvs_p": null,
"transcript": "ENST00000487791.1",
"protein_id": null,
"transcript_support_level": 1,
"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": 410,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.187T>C",
"hgvs_p": null,
"transcript": "ENST00000723616.1",
"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": 273,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.258T>C",
"hgvs_p": null,
"transcript": "ENST00000723617.1",
"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": 343,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.230T>C",
"hgvs_p": null,
"transcript": "ENST00000723618.1",
"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": 315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HBA1",
"gene_hgnc_id": 4823,
"hgvs_c": "c.-2+3A>G",
"hgvs_p": null,
"transcript": "ENST00000397797.1",
"protein_id": "ENSP00000380899.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 110,
"cds_start": -4,
"cds_end": null,
"cds_length": 333,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 504,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.202-8T>C",
"hgvs_p": null,
"transcript": "ENST00000723619.1",
"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": 279,
"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": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.202-39T>C",
"hgvs_p": null,
"transcript": "ENST00000723620.1",
"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": 248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294436",
"gene_hgnc_id": null,
"hgvs_c": "n.*192T>C",
"hgvs_p": null,
"transcript": "ENST00000723621.1",
"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": 334,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HBA1",
"gene_hgnc_id": 4823,
"dbsnp": "rs41407250",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.0000041742,
"gnomad_genomes_af": 0,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9864673018455505,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.732,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3538,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.897,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BP6",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000320868.9",
"gene_symbol": "HBA1",
"hgnc_id": 4823,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.49A>G",
"hgvs_p": "p.Lys17Glu"
},
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000723619.1",
"gene_symbol": "ENSG00000294436",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202-8T>C",
"hgvs_p": null
}
],
"clinvar_disease": "HBA1-related disorder,HEMOGLOBIN I,HEMOGLOBIN I (BURLINGTON),HEMOGLOBIN I (PHILADELPHIA),HEMOGLOBIN I (SKAMANIA),HEMOGLOBIN I (TEXAS),not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "HEMOGLOBIN I (BURLINGTON)|HEMOGLOBIN I (SKAMANIA)|HEMOGLOBIN I (PHILADELPHIA)|HEMOGLOBIN I (TEXAS)|HEMOGLOBIN I|not specified|not provided|HBA1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}