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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: 11-18729023-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=18729023&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 18729023,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000358540.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1609G>A",
"hgvs_p": "p.Gly537Ser",
"transcript": "NM_006906.2",
"protein_id": "NP_008837.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 565,
"cds_start": 1609,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1996,
"cdna_end": null,
"cdna_length": 3091,
"mane_select": "ENST00000358540.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1609G>A",
"hgvs_p": "p.Gly537Ser",
"transcript": "ENST00000358540.7",
"protein_id": "ENSP00000351342.2",
"transcript_support_level": 1,
"aa_start": 537,
"aa_end": null,
"aa_length": 565,
"cds_start": 1609,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1996,
"cdna_end": null,
"cdna_length": 3091,
"mane_select": "NM_006906.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1537G>A",
"hgvs_p": "p.Gly513Ser",
"transcript": "ENST00000396168.1",
"protein_id": "ENSP00000379471.1",
"transcript_support_level": 1,
"aa_start": 513,
"aa_end": null,
"aa_length": 541,
"cds_start": 1537,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 1705,
"cdna_end": null,
"cdna_length": 2796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1609G>A",
"hgvs_p": "p.Gly537Ser",
"transcript": "NM_032781.4",
"protein_id": "NP_116170.3",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 565,
"cds_start": 1609,
"cds_end": null,
"cds_length": 1698,
"cdna_start": 1951,
"cdna_end": null,
"cdna_length": 3046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1537G>A",
"hgvs_p": "p.Gly513Ser",
"transcript": "NM_001278238.2",
"protein_id": "NP_001265167.1",
"transcript_support_level": null,
"aa_start": 513,
"aa_end": null,
"aa_length": 541,
"cds_start": 1537,
"cds_end": null,
"cds_length": 1626,
"cdna_start": 1863,
"cdna_end": null,
"cdna_length": 2958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1513G>A",
"hgvs_p": "p.Gly505Ser",
"transcript": "NM_001039970.2",
"protein_id": "NP_001035059.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 533,
"cds_start": 1513,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1900,
"cdna_end": null,
"cdna_length": 2995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1513G>A",
"hgvs_p": "p.Gly505Ser",
"transcript": "NM_001278236.1",
"protein_id": "NP_001265165.1",
"transcript_support_level": null,
"aa_start": 505,
"aa_end": null,
"aa_length": 533,
"cds_start": 1513,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 2778,
"cdna_end": null,
"cdna_length": 3873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1513G>A",
"hgvs_p": "p.Gly505Ser",
"transcript": "ENST00000396170.5",
"protein_id": "ENSP00000379473.1",
"transcript_support_level": 2,
"aa_start": 505,
"aa_end": null,
"aa_length": 533,
"cds_start": 1513,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 2778,
"cdna_end": null,
"cdna_length": 3871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1441G>A",
"hgvs_p": "p.Gly481Ser",
"transcript": "NM_001278239.2",
"protein_id": "NP_001265168.1",
"transcript_support_level": null,
"aa_start": 481,
"aa_end": null,
"aa_length": 509,
"cds_start": 1441,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 1767,
"cdna_end": null,
"cdna_length": 2862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1021G>A",
"hgvs_p": "p.Gly341Ser",
"transcript": "ENST00000477854.5",
"protein_id": "ENSP00000435056.1",
"transcript_support_level": 5,
"aa_start": 341,
"aa_end": null,
"aa_length": 369,
"cds_start": 1021,
"cds_end": null,
"cds_length": 1110,
"cdna_start": 1731,
"cdna_end": null,
"cdna_length": 2826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.427G>A",
"hgvs_p": "p.Gly143Ser",
"transcript": "ENST00000396166.7",
"protein_id": "ENSP00000379469.3",
"transcript_support_level": 2,
"aa_start": 143,
"aa_end": null,
"aa_length": 171,
"cds_start": 427,
"cds_end": null,
"cds_length": 516,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 2299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1448G>A",
"hgvs_p": "p.Arg483Gln",
"transcript": "XM_017018434.3",
"protein_id": "XP_016873923.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 719,
"cds_start": 1448,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 2758,
"cdna_end": null,
"cdna_length": 3853,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1448G>A",
"hgvs_p": "p.Arg483Gln",
"transcript": "XM_017018435.3",
"protein_id": "XP_016873924.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 719,
"cds_start": 1448,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 2713,
"cdna_end": null,
"cdna_length": 3808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1376G>A",
"hgvs_p": "p.Arg459Gln",
"transcript": "XM_017018436.2",
"protein_id": "XP_016873925.1",
"transcript_support_level": null,
"aa_start": 459,
"aa_end": null,
"aa_length": 695,
"cds_start": 1376,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2625,
"cdna_end": null,
"cdna_length": 3720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1352G>A",
"hgvs_p": "p.Arg451Gln",
"transcript": "XM_017018437.2",
"protein_id": "XP_016873926.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 687,
"cds_start": 1352,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 2662,
"cdna_end": null,
"cdna_length": 3757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1331G>A",
"hgvs_p": "p.Arg444Gln",
"transcript": "XM_017018438.3",
"protein_id": "XP_016873927.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 680,
"cds_start": 1331,
"cds_end": null,
"cds_length": 2043,
"cdna_start": 1493,
"cdna_end": null,
"cdna_length": 2588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"hgvs_c": "c.1280G>A",
"hgvs_p": "p.Arg427Gln",
"transcript": "XM_017018439.2",
"protein_id": "XP_016873928.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 663,
"cds_start": 1280,
"cds_end": null,
"cds_length": 1992,
"cdna_start": 2529,
"cdna_end": null,
"cdna_length": 3624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF22-AS1",
"gene_hgnc_id": 55511,
"hgvs_c": "n.730-11401C>T",
"hgvs_p": null,
"transcript": "ENST00000527285.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 874,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "IGSF22-AS1",
"gene_hgnc_id": 55511,
"hgvs_c": "n.786-11401C>T",
"hgvs_p": null,
"transcript": "NR_186353.1",
"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": 2249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTPN5",
"gene_hgnc_id": 9657,
"dbsnp": "rs1173581007",
"frequency_reference_population": 0.0000020528598,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205286,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8347001671791077,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.25999999046325684,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.503,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9838,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.208,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.26,
"spliceai_max_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000358540.7",
"gene_symbol": "PTPN5",
"hgnc_id": 9657,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1609G>A",
"hgvs_p": "p.Gly537Ser"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000527285.1",
"gene_symbol": "IGSF22-AS1",
"hgnc_id": 55511,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.730-11401C>T",
"hgvs_p": null
}
],
"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
}