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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: 8-139731980-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=139731980&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 139731980,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000438773.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3278C>T",
"hgvs_p": "p.Ala1093Val",
"transcript": "NM_001160372.4",
"protein_id": "NP_001153844.1",
"transcript_support_level": null,
"aa_start": 1093,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3278,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 3394,
"cdna_end": null,
"cdna_length": 6899,
"mane_select": "ENST00000438773.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3278C>T",
"hgvs_p": "p.Ala1093Val",
"transcript": "ENST00000438773.4",
"protein_id": "ENSP00000405060.3",
"transcript_support_level": 1,
"aa_start": 1093,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3278,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 3394,
"cdna_end": null,
"cdna_length": 6899,
"mane_select": "NM_001160372.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.2807C>T",
"hgvs_p": "p.Ala936Val",
"transcript": "ENST00000520857.5",
"protein_id": "ENSP00000430116.1",
"transcript_support_level": 1,
"aa_start": 936,
"aa_end": null,
"aa_length": 991,
"cds_start": 2807,
"cds_end": null,
"cds_length": 2976,
"cdna_start": 2808,
"cdna_end": null,
"cdna_length": 3693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.1683C>T",
"hgvs_p": null,
"transcript": "ENST00000521667.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3299C>T",
"hgvs_p": "p.Ala1100Val",
"transcript": "NM_001374682.1",
"protein_id": "NP_001361611.1",
"transcript_support_level": null,
"aa_start": 1100,
"aa_end": null,
"aa_length": 1155,
"cds_start": 3299,
"cds_end": null,
"cds_length": 3468,
"cdna_start": 3415,
"cdna_end": null,
"cdna_length": 6920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3278C>T",
"hgvs_p": "p.Ala1093Val",
"transcript": "NM_031466.8",
"protein_id": "NP_113654.5",
"transcript_support_level": null,
"aa_start": 1093,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3278,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 3587,
"cdna_end": null,
"cdna_length": 7092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3278C>T",
"hgvs_p": "p.Ala1093Val",
"transcript": "ENST00000648948.2",
"protein_id": "ENSP00000498020.1",
"transcript_support_level": null,
"aa_start": 1093,
"aa_end": null,
"aa_length": 1148,
"cds_start": 3278,
"cds_end": null,
"cds_length": 3447,
"cdna_start": 3587,
"cdna_end": null,
"cdna_length": 7092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3251C>T",
"hgvs_p": "p.Ala1084Val",
"transcript": "NM_001321646.2",
"protein_id": "NP_001308575.1",
"transcript_support_level": null,
"aa_start": 1084,
"aa_end": null,
"aa_length": 1139,
"cds_start": 3251,
"cds_end": null,
"cds_length": 3420,
"cdna_start": 3367,
"cdna_end": null,
"cdna_length": 6872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3167C>T",
"hgvs_p": "p.Ala1056Val",
"transcript": "NM_001374683.1",
"protein_id": "NP_001361612.1",
"transcript_support_level": null,
"aa_start": 1056,
"aa_end": null,
"aa_length": 1111,
"cds_start": 3167,
"cds_end": null,
"cds_length": 3336,
"cdna_start": 3283,
"cdna_end": null,
"cdna_length": 6788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3134C>T",
"hgvs_p": "p.Ala1045Val",
"transcript": "NM_001374684.1",
"protein_id": "NP_001361613.1",
"transcript_support_level": null,
"aa_start": 1045,
"aa_end": null,
"aa_length": 1100,
"cds_start": 3134,
"cds_end": null,
"cds_length": 3303,
"cdna_start": 3250,
"cdna_end": null,
"cdna_length": 6755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.3545C>T",
"hgvs_p": "p.Ala1182Val",
"transcript": "XM_011517326.3",
"protein_id": "XP_011515628.1",
"transcript_support_level": null,
"aa_start": 1182,
"aa_end": null,
"aa_length": 1237,
"cds_start": 3545,
"cds_end": null,
"cds_length": 3714,
"cdna_start": 3560,
"cdna_end": null,
"cdna_length": 7065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.1898C>T",
"hgvs_p": "p.Ala633Val",
"transcript": "XM_017013894.3",
"protein_id": "XP_016869383.1",
"transcript_support_level": null,
"aa_start": 633,
"aa_end": null,
"aa_length": 688,
"cds_start": 1898,
"cds_end": null,
"cds_length": 2067,
"cdna_start": 2283,
"cdna_end": null,
"cdna_length": 5788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "c.1727C>T",
"hgvs_p": "p.Ala576Val",
"transcript": "XM_011517330.3",
"protein_id": "XP_011515632.1",
"transcript_support_level": null,
"aa_start": 576,
"aa_end": null,
"aa_length": 631,
"cds_start": 1727,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 1951,
"cdna_end": null,
"cdna_length": 5456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.365C>T",
"hgvs_p": null,
"transcript": "ENST00000519482.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.324C>T",
"hgvs_p": null,
"transcript": "ENST00000521700.5",
"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": 548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.431C>T",
"hgvs_p": null,
"transcript": "ENST00000522504.5",
"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": 665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.3440C>T",
"hgvs_p": null,
"transcript": "NR_164662.1",
"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": 6945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.*182C>T",
"hgvs_p": null,
"transcript": "ENST00000523777.5",
"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": 705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"hgvs_c": "n.*113C>T",
"hgvs_p": null,
"transcript": "ENST00000524162.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TRAPPC9",
"gene_hgnc_id": 30832,
"dbsnp": "rs750167029",
"frequency_reference_population": 0.0000355556,
"hom_count_reference_population": 1,
"allele_count_reference_population": 56,
"gnomad_exomes_af": 0.0000379542,
"gnomad_genomes_af": 0.0000131378,
"gnomad_exomes_ac": 54,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04126852750778198,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.032,
"revel_prediction": "Benign",
"alphamissense_score": 0.0826,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.877,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.13,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0029029692139796,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000438773.4",
"gene_symbol": "TRAPPC9",
"hgnc_id": 30832,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3278C>T",
"hgvs_p": "p.Ala1093Val"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}