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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: 17-49225001-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=49225001&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 49225001,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001143804.2",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.49G>T",
"hgvs_p": "p.Gly17Cys",
"transcript": "NM_178500.4",
"protein_id": "NP_848595.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 267,
"cds_start": 49,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000310544.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_178500.4"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.49G>T",
"hgvs_p": "p.Gly17Cys",
"transcript": "ENST00000310544.9",
"protein_id": "ENSP00000311925.4",
"transcript_support_level": 2,
"aa_start": 17,
"aa_end": null,
"aa_length": 267,
"cds_start": 49,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_178500.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000310544.9"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.124G>T",
"hgvs_p": "p.Gly42Cys",
"transcript": "ENST00000514112.1",
"protein_id": "ENSP00000427694.1",
"transcript_support_level": 1,
"aa_start": 42,
"aa_end": null,
"aa_length": 292,
"cds_start": 124,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514112.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.49G>T",
"hgvs_p": "p.Gly17Cys",
"transcript": "ENST00000574638.1",
"protein_id": "ENSP00000461392.1",
"transcript_support_level": 3,
"aa_start": 17,
"aa_end": null,
"aa_length": 85,
"cds_start": 49,
"cds_end": null,
"cds_length": 259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574638.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.124G>T",
"hgvs_p": "p.Gly42Cys",
"transcript": "NM_001143804.2",
"protein_id": "NP_001137276.1",
"transcript_support_level": null,
"aa_start": 42,
"aa_end": null,
"aa_length": 292,
"cds_start": 124,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001143804.2"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.124G>T",
"hgvs_p": "p.Gly42Cys",
"transcript": "ENST00000413580.5",
"protein_id": "ENSP00000406909.1",
"transcript_support_level": 2,
"aa_start": 42,
"aa_end": null,
"aa_length": 292,
"cds_start": 124,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000413580.5"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.49G>T",
"hgvs_p": "p.Gly17Cys",
"transcript": "ENST00000511066.5",
"protein_id": "ENSP00000426095.1",
"transcript_support_level": 2,
"aa_start": 17,
"aa_end": null,
"aa_length": 202,
"cds_start": 49,
"cds_end": null,
"cds_length": 611,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000511066.5"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.298G>T",
"hgvs_p": "p.Gly100Cys",
"transcript": "ENST00000503902.1",
"protein_id": "ENSP00000424406.1",
"transcript_support_level": 3,
"aa_start": 100,
"aa_end": null,
"aa_length": 165,
"cds_start": 298,
"cds_end": null,
"cds_length": 499,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503902.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.124G>T",
"hgvs_p": "p.Gly42Cys",
"transcript": "ENST00000512250.1",
"protein_id": "ENSP00000427397.1",
"transcript_support_level": 2,
"aa_start": 42,
"aa_end": null,
"aa_length": 110,
"cds_start": 124,
"cds_end": null,
"cds_length": 334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000512250.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.298G>T",
"hgvs_p": "p.Gly100Cys",
"transcript": "XM_047435504.1",
"protein_id": "XP_047291460.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 350,
"cds_start": 298,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047435504.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.298G>T",
"hgvs_p": "p.Gly100Cys",
"transcript": "XM_047435505.1",
"protein_id": "XP_047291461.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 350,
"cds_start": 298,
"cds_end": null,
"cds_length": 1053,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047435505.1"
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"hgvs_c": "c.49G>T",
"hgvs_p": "p.Gly17Cys",
"transcript": "XM_047435506.1",
"protein_id": "XP_047291462.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 267,
"cds_start": 49,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047435506.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "FLJ40194",
"gene_hgnc_id": null,
"hgvs_c": "n.292+41C>A",
"hgvs_p": null,
"transcript": "ENST00000785575.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000785575.1"
}
],
"gene_symbol": "PHOSPHO1",
"gene_hgnc_id": 16815,
"dbsnp": "rs1475583164",
"frequency_reference_population": 0.0000014597474,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000145975,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09188252687454224,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.077,
"revel_prediction": "Benign",
"alphamissense_score": 0.1223,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.022,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001143804.2",
"gene_symbol": "PHOSPHO1",
"hgnc_id": 16815,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.124G>T",
"hgvs_p": "p.Gly42Cys"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000785575.1",
"gene_symbol": "FLJ40194",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.292+41C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}