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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: 4-56476680-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=56476680&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 56476680,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000642900.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "NM_006947.4",
"protein_id": "NP_008878.3",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 671,
"cds_start": 620,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 3855,
"mane_select": "ENST00000642900.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "ENST00000642900.1",
"protein_id": "ENSP00000495128.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 671,
"cds_start": 620,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 3855,
"mane_select": "NM_006947.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "ENST00000510663.6",
"protein_id": "ENSP00000424576.1",
"transcript_support_level": 1,
"aa_start": 207,
"aa_end": null,
"aa_length": 610,
"cds_start": 620,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 2406,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "NM_001267722.2",
"protein_id": "NP_001254651.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 610,
"cds_start": 620,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 3672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.518G>A",
"hgvs_p": "p.Arg173His",
"transcript": "ENST00000505314.2",
"protein_id": "ENSP00000425190.3",
"transcript_support_level": 3,
"aa_start": 173,
"aa_end": null,
"aa_length": 333,
"cds_start": 518,
"cds_end": null,
"cds_length": 1004,
"cdna_start": 520,
"cdna_end": null,
"cdna_length": 1006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "XM_024454192.2",
"protein_id": "XP_024309960.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 548,
"cds_start": 620,
"cds_end": null,
"cds_length": 1647,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 3079,
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "n.1004G>A",
"hgvs_p": null,
"transcript": "ENST00000646537.1",
"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": 1496,
"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": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"hgvs_c": "n.639G>A",
"hgvs_p": null,
"transcript": "NR_151856.2",
"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": 3969,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000289393",
"gene_hgnc_id": null,
"hgvs_c": "n.202+1022C>T",
"hgvs_p": null,
"transcript": "ENST00000737350.1",
"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": 1060,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SRP72",
"gene_hgnc_id": 11303,
"dbsnp": "rs387907189",
"frequency_reference_population": 0.000023572411,
"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000219202,
"gnomad_genomes_af": 0.0000394187,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7457602024078369,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.68,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1035,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.735,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.01,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000642900.1",
"gene_symbol": "SRP72",
"hgnc_id": 11303,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000737350.1",
"gene_symbol": "ENSG00000289393",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.202+1022C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant aplasia and myelodysplasia,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Autosomal dominant aplasia and myelodysplasia|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}