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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: 4-88043380-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88043380&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88043380,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000297.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys",
"transcript": "NM_000297.4",
"protein_id": "NP_000288.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 968,
"cds_start": 1242,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 1341,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "ENST00000237596.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000297.4"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys",
"transcript": "ENST00000237596.7",
"protein_id": "ENSP00000237596.2",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 968,
"cds_start": 1242,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 1341,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": "NM_000297.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237596.7"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys",
"transcript": "ENST00000927447.1",
"protein_id": "ENSP00000597506.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 967,
"cds_start": 1242,
"cds_end": null,
"cds_length": 2904,
"cdna_start": 1347,
"cdna_end": null,
"cdna_length": 5089,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927447.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys",
"transcript": "ENST00000927448.1",
"protein_id": "ENSP00000597507.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 935,
"cds_start": 1242,
"cds_end": null,
"cds_length": 2808,
"cdna_start": 1344,
"cdna_end": null,
"cdna_length": 4990,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927448.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1128G>T",
"hgvs_p": "p.Trp376Cys",
"transcript": "ENST00000956200.1",
"protein_id": "ENSP00000626259.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 929,
"cds_start": 1128,
"cds_end": null,
"cds_length": 2790,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 4956,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956200.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys",
"transcript": "ENST00000956199.1",
"protein_id": "ENSP00000626258.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 775,
"cds_start": 1242,
"cds_end": null,
"cds_length": 2328,
"cdna_start": 1341,
"cdna_end": null,
"cdna_length": 4510,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956199.1"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.522G>T",
"hgvs_p": "p.Trp174Cys",
"transcript": "XM_011532029.2",
"protein_id": "XP_011530331.1",
"transcript_support_level": null,
"aa_start": 174,
"aa_end": null,
"aa_length": 728,
"cds_start": 522,
"cds_end": null,
"cds_length": 2187,
"cdna_start": 619,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532029.2"
},
{
"aa_ref": "W",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.402G>T",
"hgvs_p": "p.Trp134Cys",
"transcript": "XM_011532030.3",
"protein_id": "XP_011530332.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 688,
"cds_start": 402,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 4409,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011532030.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.-276G>T",
"hgvs_p": null,
"transcript": "ENST00000508588.5",
"protein_id": "ENSP00000427131.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 386,
"cds_start": null,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508588.5"
},
{
"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": 14,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "c.1095-3262G>T",
"hgvs_p": null,
"transcript": "NM_001440544.1",
"protein_id": "NP_001427473.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 893,
"cds_start": null,
"cds_end": null,
"cds_length": 2682,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4864,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440544.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.689G>T",
"hgvs_p": null,
"transcript": "ENST00000506367.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 693,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000506367.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"hgvs_c": "n.1341G>T",
"hgvs_p": null,
"transcript": "NR_156488.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4968,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_156488.2"
}
],
"gene_symbol": "PKD2",
"gene_hgnc_id": 9009,
"dbsnp": "rs1553925852",
"frequency_reference_population": 6.841162e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84116e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9948740005493164,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.917,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9811,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.52,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.957,
"phylop100way_prediction": "Pathogenic",
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000297.4",
"gene_symbol": "PKD2",
"hgnc_id": 9009,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1242G>T",
"hgvs_p": "p.Trp414Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}