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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: 3-10142110-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=10142110&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 10142110,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000551.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "NM_000551.4",
"protein_id": "NP_000542.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 213,
"cds_start": 263,
"cds_end": null,
"cds_length": 642,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": "ENST00000256474.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000256474.3",
"protein_id": "ENSP00000256474.3",
"transcript_support_level": 1,
"aa_start": 88,
"aa_end": null,
"aa_length": 213,
"cds_start": 263,
"cds_end": null,
"cds_length": 642,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4414,
"mane_select": "NM_000551.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000345392.3",
"protein_id": "ENSP00000344757.2",
"transcript_support_level": 1,
"aa_start": 88,
"aa_end": null,
"aa_length": 172,
"cds_start": 263,
"cds_end": null,
"cds_length": 519,
"cdna_start": 323,
"cdna_end": null,
"cdna_length": 4281,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.309G>C",
"hgvs_p": null,
"transcript": "ENST00000477538.2",
"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": 5224,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000696153.2",
"protein_id": "ENSP00000512444.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 250,
"cds_start": 263,
"cds_end": null,
"cds_length": 753,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000713811.1",
"protein_id": "ENSP00000519117.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 210,
"cds_start": 263,
"cds_end": null,
"cds_length": 633,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "NM_001354723.2",
"protein_id": "NP_001341652.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 193,
"cds_start": 263,
"cds_end": null,
"cds_length": 582,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000696143.2",
"protein_id": "ENSP00000512435.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 193,
"cds_start": 263,
"cds_end": null,
"cds_length": 582,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 4512,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "NM_198156.3",
"protein_id": "NP_937799.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 172,
"cds_start": 263,
"cds_end": null,
"cds_length": 519,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4291,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser",
"transcript": "ENST00000713982.1",
"protein_id": "ENSP00000519273.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 140,
"cds_start": 263,
"cds_end": null,
"cds_length": 423,
"cdna_start": 333,
"cdna_end": null,
"cdna_length": 4319,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.263G>C",
"hgvs_p": null,
"transcript": "ENST00000696142.2",
"protein_id": "ENSP00000512434.1",
"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": 4665,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.324G>C",
"hgvs_p": null,
"transcript": "ENST00000713813.1",
"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": 5116,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.263G>C",
"hgvs_p": null,
"transcript": "ENST00000713814.1",
"protein_id": "ENSP00000519119.1",
"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": 4462,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.333G>C",
"hgvs_p": null,
"transcript": "NR_176335.1",
"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": 4673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.219+44G>C",
"hgvs_p": null,
"transcript": "ENST00000713812.1",
"protein_id": "ENSP00000519118.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 117,
"cds_start": -4,
"cds_end": null,
"cds_length": 354,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "c.36+227G>C",
"hgvs_p": null,
"transcript": "ENST00000713815.1",
"protein_id": "ENSP00000519120.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 56,
"cds_start": -4,
"cds_end": null,
"cds_length": 171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"hgvs_c": "n.84+227G>C",
"hgvs_p": null,
"transcript": "ENST00000713816.1",
"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": 4347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "VHL",
"gene_hgnc_id": 12687,
"dbsnp": "rs119103277",
"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": 0.9937773942947388,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.945,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9957,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.043,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_000551.4",
"gene_symbol": "VHL",
"hgnc_id": 12687,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.263G>C",
"hgvs_p": "p.Trp88Ser"
}
],
"clinvar_disease": "Von Hippel-Lindau syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Von Hippel-Lindau syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}