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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: 1-1211585-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=1211585&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "TNFRSF4",
"hgnc_id": 11918,
"hgvs_c": "c.882C>T",
"hgvs_p": "p.Ala294Ala",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_001410709.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 1465,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -1.02,
"chr": "1",
"clinvar_classification": "Benign",
"clinvar_disease": "Combined immunodeficiency due to OX40 deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -1.0199999809265137,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 277,
"aa_ref": "A",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": 830,
"cds_end": null,
"cds_length": 834,
"cds_start": 804,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_003327.4",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000379236.4",
"protein_coding": true,
"protein_id": "NP_003318.1",
"strand": false,
"transcript": "NM_003327.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 277,
"aa_ref": "A",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": 830,
"cds_end": null,
"cds_length": 834,
"cds_start": 804,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000379236.4",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.804C>T",
"hgvs_p": "p.Ala268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003327.4",
"protein_coding": true,
"protein_id": "ENSP00000368538.3",
"strand": false,
"transcript": "ENST00000379236.4",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 355,
"aa_ref": "R",
"aa_start": 305,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1184,
"cdna_start": 939,
"cds_end": null,
"cds_length": 1068,
"cds_start": 913,
"consequences": [
"stop_gained"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699971.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.913C>T",
"hgvs_p": "p.Arg305*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514728.1",
"strand": false,
"transcript": "ENST00000699971.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 253,
"aa_ref": "R",
"aa_start": 203,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 878,
"cdna_start": 633,
"cds_end": null,
"cds_length": 762,
"cds_start": 607,
"consequences": [
"stop_gained"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699976.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.607C>T",
"hgvs_p": "p.Arg203*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514732.1",
"strand": false,
"transcript": "ENST00000699976.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 303,
"aa_ref": "A",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1153,
"cdna_start": 908,
"cds_end": null,
"cds_length": 912,
"cds_start": 882,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001410709.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.882C>T",
"hgvs_p": "p.Ala294Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397638.1",
"strand": false,
"transcript": "NM_001410709.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 303,
"aa_ref": "A",
"aa_start": 294,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1153,
"cdna_start": 908,
"cds_end": null,
"cds_length": 912,
"cds_start": 882,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699974.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.882C>T",
"hgvs_p": "p.Ala294Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514730.1",
"strand": false,
"transcript": "ENST00000699974.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 298,
"aa_ref": "A",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1152,
"cdna_start": 893,
"cds_end": null,
"cds_length": 897,
"cds_start": 867,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699969.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.867C>T",
"hgvs_p": "p.Ala289Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514726.1",
"strand": false,
"transcript": "ENST00000699969.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 234,
"aa_ref": "A",
"aa_start": 225,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 946,
"cdna_start": 701,
"cds_end": null,
"cds_length": 705,
"cds_start": 675,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699977.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.675C>T",
"hgvs_p": "p.Ala225Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514733.1",
"strand": false,
"transcript": "ENST00000699977.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 189,
"aa_ref": "A",
"aa_start": 180,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 811,
"cdna_start": 566,
"cds_end": null,
"cds_length": 570,
"cds_start": 540,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000699975.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.540C>T",
"hgvs_p": "p.Ala180Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514731.1",
"strand": false,
"transcript": "ENST00000699975.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 307,
"aa_ref": "A",
"aa_start": 298,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1516,
"cdna_start": 1271,
"cds_end": null,
"cds_length": 924,
"cds_start": 894,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011542074.3",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.894C>T",
"hgvs_p": "p.Ala298Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011540376.1",
"strand": false,
"transcript": "XM_011542074.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 281,
"aa_ref": "A",
"aa_start": 272,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1438,
"cdna_start": 1193,
"cds_end": null,
"cds_length": 846,
"cds_start": 816,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011542076.3",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.816C>T",
"hgvs_p": "p.Ala272Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011540378.1",
"strand": false,
"transcript": "XM_011542076.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 203,
"aa_ref": "A",
"aa_start": 194,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 954,
"cdna_start": 709,
"cds_end": null,
"cds_length": 612,
"cds_start": 582,
"consequences": [
"synonymous_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_011542077.3",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "c.582C>T",
"hgvs_p": "p.Ala194Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011540379.1",
"strand": false,
"transcript": "XM_011542077.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1707,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000497869.5",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.1462C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000497869.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1012,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000699970.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.761C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000514727.1",
"strand": false,
"transcript": "ENST00000699970.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1644,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699972.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.1399C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000699972.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1067,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000699973.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.*184C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000514729.1",
"strand": false,
"transcript": "ENST00000699973.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 959,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000699978.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.692C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000514734.1",
"strand": false,
"transcript": "ENST00000699978.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1002,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000699979.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.737C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000514735.1",
"strand": false,
"transcript": "ENST00000699979.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1067,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000699973.1",
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"hgvs_c": "n.*184C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000514729.1",
"strand": false,
"transcript": "ENST00000699973.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs35160621",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000964251,
"gene_hgnc_id": 11918,
"gene_symbol": "TNFRSF4",
"gnomad_exomes_ac": 668,
"gnomad_exomes_af": 0.000488613,
"gnomad_exomes_homalt": 6,
"gnomad_genomes_ac": 797,
"gnomad_genomes_af": 0.00523722,
"gnomad_genomes_homalt": 6,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 12,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Combined immunodeficiency due to OX40 deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -11.301,
"pos": 1211585,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001410709.1"
}
]
}