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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: 16-173580-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=173580&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 173580,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000251595.11",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "NM_000517.6",
"protein_id": "NP_000508.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 142,
"cds_start": 409,
"cds_end": null,
"cds_length": 429,
"cdna_start": 446,
"cdna_end": null,
"cdna_length": 576,
"mane_select": "ENST00000251595.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met",
"transcript": "ENST00000251595.11",
"protein_id": "ENSP00000251595.6",
"transcript_support_level": 1,
"aa_start": 137,
"aa_end": null,
"aa_length": 142,
"cds_start": 409,
"cds_end": null,
"cds_length": 429,
"cdna_start": 446,
"cdna_end": null,
"cdna_length": 576,
"mane_select": "NM_000517.6",
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"hgvs_c": "n.545C>A",
"hgvs_p": null,
"transcript": "ENST00000482565.1",
"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": 640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"hgvs_c": "c.313C>A",
"hgvs_p": "p.Leu105Met",
"transcript": "ENST00000397806.1",
"protein_id": "ENSP00000380908.1",
"transcript_support_level": 2,
"aa_start": 105,
"aa_end": null,
"aa_length": 110,
"cds_start": 313,
"cds_end": null,
"cds_length": 333,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 513,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294455",
"gene_hgnc_id": null,
"hgvs_c": "n.131G>T",
"hgvs_p": null,
"transcript": "ENST00000723699.1",
"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": false,
"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": "ENSG00000294455",
"gene_hgnc_id": null,
"hgvs_c": "n.131G>T",
"hgvs_p": null,
"transcript": "ENST00000723700.1",
"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": 283,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294455",
"gene_hgnc_id": null,
"hgvs_c": "n.126G>T",
"hgvs_p": null,
"transcript": "ENST00000723701.1",
"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": 221,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294455",
"gene_hgnc_id": null,
"hgvs_c": "n.131G>T",
"hgvs_p": null,
"transcript": "ENST00000723702.1",
"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": 236,
"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": "ENSG00000294455",
"gene_hgnc_id": null,
"hgvs_c": "n.143G>T",
"hgvs_p": null,
"transcript": "ENST00000723703.1",
"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": 253,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"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": "HBA2",
"gene_hgnc_id": 4824,
"hgvs_c": "c.*117C>A",
"hgvs_p": null,
"transcript": "ENST00000484216.1",
"protein_id": "ENSP00000495899.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 132,
"cds_start": -4,
"cds_end": null,
"cds_length": 401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"dbsnp": "rs41364652",
"frequency_reference_population": 0.000014923609,
"hom_count_reference_population": 3,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.00000548269,
"gnomad_genomes_af": 0.000107345,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8609768152236938,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.771,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.65,
"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": "Uncertain_significance",
"acmg_criteria": "PM1,PM5,PP3_Moderate,BP6,BS2",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 5,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM5",
"PP3_Moderate",
"BP6",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000251595.11",
"gene_symbol": "HBA2",
"hgnc_id": 4824,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.409C>A",
"hgvs_p": "p.Leu137Met"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000723699.1",
"gene_symbol": "ENSG00000294455",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.131G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}