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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: 3-120633316-CTC-TA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=120633316&ref=CTC&alt=TA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 120633316,
"ref": "CTC",
"alt": "TA",
"effect": "frameshift_variant,missense_variant",
"transcript": "ENST00000283871.10",
"consequences": [
{
"aa_ref": "MS",
"aa_alt": "I?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.1017_1019delGAGinsTA",
"hgvs_p": "p.Met339fs",
"transcript": "NM_000187.4",
"protein_id": "NP_000178.2",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 445,
"cds_start": 1017,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1147,
"cdna_end": null,
"cdna_length": 1674,
"mane_select": "ENST00000283871.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "MS",
"aa_alt": "I?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.1017_1019delGAGinsTA",
"hgvs_p": "p.Met339fs",
"transcript": "ENST00000283871.10",
"protein_id": "ENSP00000283871.5",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 445,
"cds_start": 1017,
"cds_end": null,
"cds_length": 1338,
"cdna_start": 1147,
"cdna_end": null,
"cdna_length": 1674,
"mane_select": "NM_000187.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "MS",
"aa_alt": "I?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.792_794delGAGinsTA",
"hgvs_p": "p.Met264fs",
"transcript": "XM_005247412.3",
"protein_id": "XP_005247469.1",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 370,
"cds_start": 792,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 922,
"cdna_end": null,
"cdna_length": 1449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "MS",
"aa_alt": "I?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant",
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.594_596delGAGinsTA",
"hgvs_p": "p.Met198fs",
"transcript": "XM_017006277.3",
"protein_id": "XP_016861766.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 304,
"cds_start": 594,
"cds_end": null,
"cds_length": 915,
"cdna_start": 1095,
"cdna_end": null,
"cdna_length": 1622,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "n.357_359delGAGinsTA",
"hgvs_p": null,
"transcript": "ENST00000470321.1",
"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": 528,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "n.296_*1delGAGinsTA",
"hgvs_p": null,
"transcript": "ENST00000492108.5",
"protein_id": "ENSP00000419838.1",
"transcript_support_level": 2,
"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": 631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "n.296_*1delGAGinsTA",
"hgvs_p": null,
"transcript": "ENST00000492108.5",
"protein_id": "ENSP00000419838.1",
"transcript_support_level": 2,
"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": 631,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*262_*264delGAGinsTA",
"hgvs_p": null,
"transcript": "ENST00000494453.1",
"protein_id": "ENSP00000419163.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 144,
"cds_start": -4,
"cds_end": null,
"cds_length": 435,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 683,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*314_*316delGAGinsTA",
"hgvs_p": null,
"transcript": "ENST00000475447.2",
"protein_id": "ENSP00000417977.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 87,
"cds_start": -4,
"cds_end": null,
"cds_length": 264,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 565,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*262_*264delGAGinsTA",
"hgvs_p": null,
"transcript": "XM_005247413.3",
"protein_id": "XP_005247470.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 338,
"cds_start": -4,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1392,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*267_*269delGAGinsTA",
"hgvs_p": null,
"transcript": "XM_011512746.3",
"protein_id": "XP_011511048.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 294,
"cds_start": -4,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1265,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*262_*264delGAGinsTA",
"hgvs_p": null,
"transcript": "XM_047448058.1",
"protein_id": "XP_047304014.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 263,
"cds_start": -4,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1167,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"hgvs_c": "c.*267_*269delGAGinsTA",
"hgvs_p": null,
"transcript": "XM_047448059.1",
"protein_id": "XP_047304015.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 219,
"cds_start": -4,
"cds_end": null,
"cds_length": 660,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HGD",
"gene_hgnc_id": 4892,
"dbsnp": "rs1057517081",
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 7.396,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PVS1",
"PM2",
"PP2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000283871.10",
"gene_symbol": "HGD",
"hgnc_id": 4892,
"effects": [
"frameshift_variant",
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1017_1019delGAGinsTA",
"hgvs_p": "p.Met339fs"
}
],
"clinvar_disease": "Alkaptonuria,HGD-related disorder",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Alkaptonuria|HGD-related disorder",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}