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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: 6-112207031-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=112207031&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 112207031,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000230538.12",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "NM_001105206.3",
"protein_id": "NP_001098676.2",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1823,
"cds_start": 412,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 7228,
"mane_select": "ENST00000230538.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "ENST00000230538.12",
"protein_id": "ENSP00000230538.7",
"transcript_support_level": 1,
"aa_start": 138,
"aa_end": null,
"aa_length": 1823,
"cds_start": 412,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 7228,
"mane_select": "NM_001105206.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "ENST00000389463.9",
"protein_id": "ENSP00000374114.4",
"transcript_support_level": 1,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 6381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "ENST00000522006.5",
"protein_id": "ENSP00000429488.1",
"transcript_support_level": 1,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 822,
"cdna_end": null,
"cdna_length": 6438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "NM_001105207.3",
"protein_id": "NP_001098677.2",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 7224,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "NM_002290.5",
"protein_id": "NP_002281.3",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 662,
"cdna_end": null,
"cdna_length": 7207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "ENST00000424408.6",
"protein_id": "ENSP00000416470.2",
"transcript_support_level": 5,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 800,
"cdna_end": null,
"cdna_length": 5983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "ENST00000521398.5",
"protein_id": "ENSP00000430336.1",
"transcript_support_level": 5,
"aa_start": 138,
"aa_end": null,
"aa_length": 330,
"cds_start": 412,
"cds_end": null,
"cds_length": 995,
"cdna_start": 747,
"cdna_end": null,
"cdna_length": 1330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_005266983.5",
"protein_id": "XP_005267040.2",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1823,
"cds_start": 412,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 7245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_005266984.5",
"protein_id": "XP_005267041.2",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1823,
"cds_start": 412,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 682,
"cdna_end": null,
"cdna_length": 7248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_047418769.1",
"protein_id": "XP_047274725.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1823,
"cds_start": 412,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 782,
"cdna_end": null,
"cdna_length": 7348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_017010854.3",
"protein_id": "XP_016866343.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 682,
"cdna_end": null,
"cdna_length": 7227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_047418770.1",
"protein_id": "XP_047274726.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1816,
"cds_start": 412,
"cds_end": null,
"cds_length": 5451,
"cdna_start": 801,
"cdna_end": null,
"cdna_length": 7346,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr",
"transcript": "XM_047418771.1",
"protein_id": "XP_047274727.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 1279,
"cds_start": 412,
"cds_end": null,
"cds_length": 3840,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 4155,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "n.197C>T",
"hgvs_p": null,
"transcript": "ENST00000423735.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 331,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "n.336C>T",
"hgvs_p": null,
"transcript": "ENST00000524032.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 559,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"hgvs_c": "c.*92C>T",
"hgvs_p": null,
"transcript": "ENST00000519932.5",
"protein_id": "ENSP00000428583.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": -4,
"cds_end": null,
"cds_length": 320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LAMA4",
"gene_hgnc_id": 6484,
"dbsnp": "rs727503113",
"frequency_reference_population": 0.000045235465,
"hom_count_reference_population": 0,
"allele_count_reference_population": 73,
"gnomad_exomes_af": 0.000045838,
"gnomad_genomes_af": 0.0000394451,
"gnomad_exomes_ac": 67,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05153918266296387,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.109,
"revel_prediction": "Benign",
"alphamissense_score": 0.0743,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.513,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000230538.12",
"gene_symbol": "LAMA4",
"hgnc_id": 6484,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.412C>T",
"hgvs_p": "p.His138Tyr"
}
],
"clinvar_disease": "Cardiovascular phenotype,Dilated cardiomyopathy 1JJ,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "not specified|Cardiovascular phenotype|Dilated cardiomyopathy 1JJ|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}