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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: 16-173598-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=173598&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 173598,
"ref": "T",
"alt": "C",
"effect": "stop_lost",
"transcript": "NM_000517.6",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"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.427T>C",
"hgvs_p": "p.Ter143Glnext*?",
"transcript": "NM_000517.6",
"protein_id": "NP_000508.1",
"transcript_support_level": null,
"aa_start": 143,
"aa_end": null,
"aa_length": 142,
"cds_start": 427,
"cds_end": null,
"cds_length": 429,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 576,
"mane_select": "ENST00000251595.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000517.6"
},
{
"aa_ref": "*",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"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.427T>C",
"hgvs_p": "p.Ter143Glnext*?",
"transcript": "ENST00000251595.11",
"protein_id": "ENSP00000251595.6",
"transcript_support_level": 1,
"aa_start": 143,
"aa_end": null,
"aa_length": 142,
"cds_start": 427,
"cds_end": null,
"cds_length": 429,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 576,
"mane_select": "NM_000517.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000251595.11"
},
{
"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.563T>C",
"hgvs_p": null,
"transcript": "ENST00000482565.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 640,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000482565.1"
},
{
"aa_ref": "*",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"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.343T>C",
"hgvs_p": "p.Ter115Glnext*?",
"transcript": "ENST00000866237.1",
"protein_id": "ENSP00000536296.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 114,
"cds_start": 343,
"cds_end": null,
"cds_length": 345,
"cdna_start": 380,
"cdna_end": null,
"cdna_length": 492,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866237.1"
},
{
"aa_ref": "*",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_lost"
],
"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.331T>C",
"hgvs_p": "p.Ter111Glnext*?",
"transcript": "ENST00000397806.1",
"protein_id": "ENSP00000380908.1",
"transcript_support_level": 2,
"aa_start": 111,
"aa_end": null,
"aa_length": 110,
"cds_start": 331,
"cds_end": null,
"cds_length": 333,
"cdna_start": 401,
"cdna_end": null,
"cdna_length": 513,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000397806.1"
},
{
"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.113A>G",
"hgvs_p": null,
"transcript": "ENST00000723699.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 248,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723699.1"
},
{
"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.113A>G",
"hgvs_p": null,
"transcript": "ENST00000723700.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 283,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723700.1"
},
{
"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.108A>G",
"hgvs_p": null,
"transcript": "ENST00000723701.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 221,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723701.1"
},
{
"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.113A>G",
"hgvs_p": null,
"transcript": "ENST00000723702.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 236,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723702.1"
},
{
"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.125A>G",
"hgvs_p": null,
"transcript": "ENST00000723703.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 253,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000723703.1"
},
{
"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.*135T>C",
"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": null,
"cds_end": null,
"cds_length": 401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 403,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000484216.1"
}
],
"gene_symbol": "HBA2",
"gene_hgnc_id": 4824,
"dbsnp": "rs41464951",
"frequency_reference_population": 0.00002238444,
"hom_count_reference_population": 1,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000205607,
"gnomad_genomes_af": 0.0000402236,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.10000000149011612,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.118,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM4,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PS3",
"PM4",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000517.6",
"gene_symbol": "HBA2",
"hgnc_id": 4824,
"effects": [
"stop_lost"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.427T>C",
"hgvs_p": "p.Ter143Glnext*?"
},
{
"score": 11,
"benign_score": 1,
"pathogenic_score": 12,
"criteria": [
"PS3",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "ENST00000723699.1",
"gene_symbol": "ENSG00000294455",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.113A>G",
"hgvs_p": null
}
],
"clinvar_disease": " 7, familial, nondeletional,Erythrocytosis,Heinz body anemia,Hemoglobin H disease,Hemoglobin constant spring,alpha Thalassemia,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:12 LP:1 O:2",
"phenotype_combined": "Hemoglobin H disease, nondeletional|alpha Thalassemia|not provided|Hemoglobin constant spring|Hemoglobin H disease|Erythrocytosis, familial, 7;Heinz body anemia;Hemoglobin H disease;alpha Thalassemia",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}