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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: 5-83579981-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=83579981&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 83579981,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000265077.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.9882C>T",
"hgvs_p": "p.Val3294Val",
"transcript": "NM_004385.5",
"protein_id": "NP_004376.2",
"transcript_support_level": null,
"aa_start": 3294,
"aa_end": null,
"aa_length": 3396,
"cds_start": 9882,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 10168,
"cdna_end": null,
"cdna_length": 12345,
"mane_select": "ENST00000265077.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.9882C>T",
"hgvs_p": "p.Val3294Val",
"transcript": "ENST00000265077.8",
"protein_id": "ENSP00000265077.3",
"transcript_support_level": 1,
"aa_start": 3294,
"aa_end": null,
"aa_length": 3396,
"cds_start": 9882,
"cds_end": null,
"cds_length": 10191,
"cdna_start": 10168,
"cdna_end": null,
"cdna_length": 12345,
"mane_select": "NM_004385.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.6921C>T",
"hgvs_p": "p.Val2307Val",
"transcript": "ENST00000343200.9",
"protein_id": "ENSP00000340062.5",
"transcript_support_level": 1,
"aa_start": 2307,
"aa_end": null,
"aa_length": 2409,
"cds_start": 6921,
"cds_end": null,
"cds_length": 7230,
"cdna_start": 7277,
"cdna_end": null,
"cdna_length": 9455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.4620C>T",
"hgvs_p": "p.Val1540Val",
"transcript": "ENST00000342785.8",
"protein_id": "ENSP00000342768.4",
"transcript_support_level": 1,
"aa_start": 1540,
"aa_end": null,
"aa_length": 1642,
"cds_start": 4620,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 4976,
"cdna_end": null,
"cdna_length": 7154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.4476C>T",
"hgvs_p": "p.Val1492Val",
"transcript": "ENST00000512590.6",
"protein_id": "ENSP00000425959.2",
"transcript_support_level": 1,
"aa_start": 1492,
"aa_end": null,
"aa_length": 1594,
"cds_start": 4476,
"cds_end": null,
"cds_length": 4785,
"cdna_start": 4886,
"cdna_end": null,
"cdna_length": 5923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.1659C>T",
"hgvs_p": "p.Val553Val",
"transcript": "ENST00000502527.2",
"protein_id": "ENSP00000421362.2",
"transcript_support_level": 1,
"aa_start": 553,
"aa_end": null,
"aa_length": 655,
"cds_start": 1659,
"cds_end": null,
"cds_length": 1968,
"cdna_start": 1764,
"cdna_end": null,
"cdna_length": 2087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "n.7272C>T",
"hgvs_p": null,
"transcript": "ENST00000513016.5",
"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": 8483,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.6921C>T",
"hgvs_p": "p.Val2307Val",
"transcript": "NM_001164097.2",
"protein_id": "NP_001157569.1",
"transcript_support_level": null,
"aa_start": 2307,
"aa_end": null,
"aa_length": 2409,
"cds_start": 6921,
"cds_end": null,
"cds_length": 7230,
"cdna_start": 7207,
"cdna_end": null,
"cdna_length": 9384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.4620C>T",
"hgvs_p": "p.Val1540Val",
"transcript": "NM_001164098.2",
"protein_id": "NP_001157570.1",
"transcript_support_level": null,
"aa_start": 1540,
"aa_end": null,
"aa_length": 1642,
"cds_start": 4620,
"cds_end": null,
"cds_length": 4929,
"cdna_start": 4906,
"cdna_end": null,
"cdna_length": 7083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "c.1659C>T",
"hgvs_p": "p.Val553Val",
"transcript": "NM_001126336.3",
"protein_id": "NP_001119808.1",
"transcript_support_level": null,
"aa_start": 553,
"aa_end": null,
"aa_length": 655,
"cds_start": 1659,
"cds_end": null,
"cds_length": 1968,
"cdna_start": 1945,
"cdna_end": null,
"cdna_length": 4122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"hgvs_c": "n.391C>T",
"hgvs_p": null,
"transcript": "ENST00000505615.1",
"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": 810,
"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": "VCAN-AS1",
"gene_hgnc_id": 40163,
"hgvs_c": "n.228+1112G>A",
"hgvs_p": null,
"transcript": "ENST00000513899.1",
"protein_id": null,
"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": 453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VCAN",
"gene_hgnc_id": 2464,
"dbsnp": "rs308365",
"frequency_reference_population": 0.9674418,
"hom_count_reference_population": 755470,
"allele_count_reference_population": 1561511,
"gnomad_exomes_af": 0.966765,
"gnomad_genomes_af": 0.973937,
"gnomad_exomes_ac": 1413159,
"gnomad_genomes_ac": 148352,
"gnomad_exomes_homalt": 683207,
"gnomad_genomes_homalt": 72263,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.014000000432133675,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.797,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000641695787107348,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000265077.8",
"gene_symbol": "VCAN",
"hgnc_id": 2464,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.9882C>T",
"hgvs_p": "p.Val3294Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000513899.1",
"gene_symbol": "VCAN-AS1",
"hgnc_id": 40163,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.228+1112G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Vitreoretinopathy,Wagner syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|Wagner syndrome|Vitreoretinopathy|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}