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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: 9-137233404-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=137233404&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 137233404,
"ref": "G",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000673835.1",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "NM_001177316.2",
"protein_id": "NP_001170787.2",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 2016,
"mane_select": "ENST00000673835.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "ENST00000673835.1",
"protein_id": "ENSP00000501114.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 2016,
"mane_select": "NM_001177316.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "NM_001177317.2",
"protein_id": "NP_001170788.2",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 980,
"cdna_end": null,
"cdna_length": 2163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "NM_080877.3",
"protein_id": "NP_543153.2",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 942,
"cdna_end": null,
"cdna_length": 2125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "ENST00000361134.2",
"protein_id": "ENSP00000355353.2",
"transcript_support_level": 2,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 942,
"cdna_end": null,
"cdna_length": 2124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "ENST00000538474.5",
"protein_id": "ENSP00000442397.1",
"transcript_support_level": 5,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 980,
"cdna_end": null,
"cdna_length": 2162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "ENST00000673865.1",
"protein_id": "ENSP00000501101.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 352,
"cds_start": 756,
"cds_end": null,
"cds_length": 1059,
"cdna_start": 980,
"cdna_end": null,
"cdna_length": 1283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422785.1",
"protein_id": "XP_047278741.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 1173,
"cdna_end": null,
"cdna_length": 2295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422786.1",
"protein_id": "XP_047278742.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 1208,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422787.1",
"protein_id": "XP_047278743.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 2146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422788.1",
"protein_id": "XP_047278744.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 935,
"cdna_end": null,
"cdna_length": 2057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422789.1",
"protein_id": "XP_047278745.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 2054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422790.1",
"protein_id": "XP_047278746.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 658,
"cds_start": 855,
"cds_end": null,
"cds_length": 1977,
"cdna_start": 1027,
"cdna_end": null,
"cdna_length": 2149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422791.1",
"protein_id": "XP_047278747.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 640,
"cds_start": 855,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1355,
"cdna_end": null,
"cdna_length": 2921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.855G>T",
"hgvs_p": "p.Gln285His",
"transcript": "XM_047422792.1",
"protein_id": "XP_047278748.1",
"transcript_support_level": null,
"aa_start": 285,
"aa_end": null,
"aa_length": 632,
"cds_start": 855,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1355,
"cdna_end": null,
"cdna_length": 2538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "XM_011518258.2",
"protein_id": "XP_011516560.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 625,
"cds_start": 756,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 836,
"cdna_end": null,
"cdna_length": 1958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "XM_011518259.2",
"protein_id": "XP_011516561.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 625,
"cds_start": 756,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 942,
"cdna_end": null,
"cdna_length": 2064,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "XM_011518260.2",
"protein_id": "XP_011516562.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 625,
"cds_start": 756,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 833,
"cdna_end": null,
"cdna_length": 1955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His",
"transcript": "XM_047422793.1",
"protein_id": "XP_047278749.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 599,
"cds_start": 756,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1175,
"cdna_end": null,
"cdna_length": 2358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC34A3",
"gene_hgnc_id": 20305,
"dbsnp": "rs121918239",
"frequency_reference_population": 0.000006214946,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000621495,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.808199405670166,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9359999895095825,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.291,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5618,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.26,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.964,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.83,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.998613883511783,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000673835.1",
"gene_symbol": "SLC34A3",
"hgnc_id": 20305,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "SD,AR",
"hgvs_c": "c.756G>T",
"hgvs_p": "p.Gln252His"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}