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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: 4-83308885-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=83308885&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HPSE",
"hgnc_id": 5164,
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_006665.6",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 83,
"alphamissense_prediction": null,
"alphamissense_score": 0.9296,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.23,
"chr": "4",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9560450315475464,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 543,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4581,
"cdna_start": 1117,
"cds_end": null,
"cds_length": 1632,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001098540.3",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000311412.10",
"protein_coding": true,
"protein_id": "NP_001092010.1",
"strand": false,
"transcript": "NM_001098540.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 543,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4581,
"cdna_start": 1117,
"cds_end": null,
"cds_length": 1632,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000311412.10",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001098540.3",
"protein_coding": true,
"protein_id": "ENSP00000308107.5",
"strand": false,
"transcript": "ENST00000311412.10",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 543,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4652,
"cdna_start": 1188,
"cds_end": null,
"cds_length": 1632,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000405413.6",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384262.2",
"strand": false,
"transcript": "ENST00000405413.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 485,
"aa_ref": "G",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 877,
"cds_end": null,
"cds_length": 1458,
"cds_start": 877,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000513463.1",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Gly293Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421365.1",
"strand": false,
"transcript": "ENST00000513463.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 469,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1571,
"cdna_start": null,
"cds_end": null,
"cds_length": 1410,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000512196.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.984+517G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423265.1",
"strand": false,
"transcript": "ENST00000512196.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1624,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000507150.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "n.*201G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426139.1",
"strand": false,
"transcript": "ENST00000507150.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000508891.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "n.*201G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421827.1",
"strand": false,
"transcript": "ENST00000508891.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1678,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000509906.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "n.1051G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421038.1",
"strand": false,
"transcript": "ENST00000509906.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1624,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000507150.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "n.*201G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000426139.1",
"strand": false,
"transcript": "ENST00000507150.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1450,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000508891.5",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "n.*201G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421827.1",
"strand": false,
"transcript": "ENST00000508891.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 543,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4652,
"cdna_start": 1188,
"cds_end": null,
"cds_length": 1632,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_006665.6",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_006656.2",
"strand": false,
"transcript": "NM_006665.6",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 534,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1710,
"cdna_start": 1136,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000909494.1",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579553.1",
"strand": false,
"transcript": "ENST00000909494.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 498,
"aa_ref": "G",
"aa_start": 351,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2544,
"cdna_start": 1051,
"cds_end": null,
"cds_length": 1497,
"cds_start": 1051,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000681769.1",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.1051G>A",
"hgvs_p": "p.Gly351Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000506434.1",
"strand": false,
"transcript": "ENST00000681769.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 485,
"aa_ref": "G",
"aa_start": 293,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4372,
"cdna_start": 908,
"cds_end": null,
"cds_length": 1458,
"cds_start": 877,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001199830.1",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.877G>A",
"hgvs_p": "p.Gly293Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186759.1",
"strand": false,
"transcript": "NM_001199830.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 469,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4430,
"cdna_start": null,
"cds_end": null,
"cds_length": 1410,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001166498.3",
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"hgvs_c": "c.984+517G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001159970.1",
"strand": false,
"transcript": "NM_001166498.3",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs769081542",
"effect": "missense_variant",
"frequency_reference_population": 0.00005142516,
"gene_hgnc_id": 5164,
"gene_symbol": "HPSE",
"gnomad_exomes_ac": 72,
"gnomad_exomes_af": 0.000049253,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 11,
"gnomad_genomes_af": 0.0000722942,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.997,
"pos": 83308885,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.764,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.029999999329447746,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_006665.6"
}
]
}