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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: 12-65828077-CA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=65828077&ref=CA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 65828077,
"ref": "CA",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000403681.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "NM_003483.6",
"protein_id": "NP_003474.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 109,
"cds_start": 189,
"cds_end": null,
"cds_length": 330,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 4117,
"mane_select": "ENST00000403681.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000403681.7",
"protein_id": "ENSP00000384026.2",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 109,
"cds_start": 189,
"cds_end": null,
"cds_length": 330,
"cdna_start": 977,
"cdna_end": null,
"cdna_length": 4117,
"mane_select": "NM_003483.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000536545.5",
"protein_id": "ENSP00000437621.1",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 147,
"cds_start": 189,
"cds_end": null,
"cds_length": 444,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000354636.7",
"protein_id": "ENSP00000346658.3",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 106,
"cds_start": 189,
"cds_end": null,
"cds_length": 321,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000541363.5",
"protein_id": "ENSP00000439317.1",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 99,
"cds_start": 189,
"cds_end": null,
"cds_length": 300,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 8094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000425208.6",
"protein_id": "ENSP00000407306.2",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 92,
"cds_start": 189,
"cds_end": null,
"cds_length": 279,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000393578.7",
"protein_id": "ENSP00000377206.3",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 90,
"cds_start": 189,
"cds_end": null,
"cds_length": 273,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1993,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "n.189delA",
"hgvs_p": null,
"transcript": "ENST00000537275.5",
"protein_id": "ENSP00000437747.1",
"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": 1508,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "n.189delA",
"hgvs_p": null,
"transcript": "ENST00000537429.5",
"protein_id": "ENSP00000443372.1",
"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": 1527,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "n.649delA",
"hgvs_p": null,
"transcript": "ENST00000545998.1",
"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": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "NM_001300919.1",
"protein_id": "NP_001287848.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 147,
"cds_start": 189,
"cds_end": null,
"cds_length": 444,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "NM_001300918.1",
"protein_id": "NP_001287847.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 118,
"cds_start": 189,
"cds_end": null,
"cds_length": 357,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "ENST00000393577.7",
"protein_id": "ENSP00000377205.3",
"transcript_support_level": 3,
"aa_start": 63,
"aa_end": null,
"aa_length": 118,
"cds_start": 189,
"cds_end": null,
"cds_length": 357,
"cdna_start": 337,
"cdna_end": null,
"cdna_length": 611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "NM_003484.1",
"protein_id": "NP_003475.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 106,
"cds_start": 189,
"cds_end": null,
"cds_length": 321,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs",
"transcript": "NM_001330190.1",
"protein_id": "NP_001317119.1",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 90,
"cds_start": 189,
"cds_end": null,
"cds_length": 273,
"cdna_start": 1000,
"cdna_end": null,
"cdna_length": 1993,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"hgvs_c": "n.78delA",
"hgvs_p": null,
"transcript": "ENST00000539662.1",
"protein_id": "ENSP00000440919.1",
"transcript_support_level": 3,
"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": 485,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HMGA2",
"gene_hgnc_id": 5009,
"dbsnp": "rs1114167320",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.802,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000403681.7",
"gene_symbol": "HMGA2",
"hgnc_id": 5009,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.189delA",
"hgvs_p": "p.Ala64fs"
}
],
"clinvar_disease": "Silver-Russell syndrome 1,Silver-Russell syndrome 5",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Silver-Russell syndrome 1|Silver-Russell syndrome 5",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}