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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: 17-3729542-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=3729542&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ITGAE",
"hgnc_id": 6147,
"hgvs_c": "c.2848C>T",
"hgvs_p": "p.Arg950Trp",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_002208.5",
"verdict": "Benign"
},
{
"benign_score": 8,
"criteria": [
"BA1"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000262358",
"hgnc_id": null,
"hgvs_c": "n.182G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -8,
"transcript": "ENST00000575043.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BA1",
"acmg_score": -8,
"allele_count_reference_population": 521696,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1261,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"chr": "17",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.00040462613105773926,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1179,
"aa_ref": "R",
"aa_start": 950,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3803,
"cdna_start": 2892,
"cds_end": null,
"cds_length": 3540,
"cds_start": 2848,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "NM_002208.5",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2848C>T",
"hgvs_p": "p.Arg950Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263087.9",
"protein_coding": true,
"protein_id": "NP_002199.3",
"strand": false,
"transcript": "NM_002208.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1179,
"aa_ref": "R",
"aa_start": 950,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3803,
"cdna_start": 2892,
"cds_end": null,
"cds_length": 3540,
"cds_start": 2848,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000263087.9",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2848C>T",
"hgvs_p": "p.Arg950Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002208.5",
"protein_coding": true,
"protein_id": "ENSP00000263087.4",
"strand": false,
"transcript": "ENST00000263087.9",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1211,
"aa_ref": "R",
"aa_start": 982,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3895,
"cdna_start": 2986,
"cds_end": null,
"cds_length": 3636,
"cds_start": 2944,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000949198.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2944C>T",
"hgvs_p": "p.Arg982Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619257.1",
"strand": false,
"transcript": "ENST00000949198.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1200,
"aa_ref": "R",
"aa_start": 971,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3864,
"cdna_start": 2953,
"cds_end": null,
"cds_length": 3603,
"cds_start": 2911,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000868856.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2911C>T",
"hgvs_p": "p.Arg971Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538915.1",
"strand": false,
"transcript": "ENST00000868856.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1171,
"aa_ref": "R",
"aa_start": 942,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3771,
"cdna_start": 2868,
"cds_end": null,
"cds_length": 3516,
"cds_start": 2824,
"consequences": [
"missense_variant"
],
"exon_count": 31,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000868857.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2824C>T",
"hgvs_p": "p.Arg942Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538916.1",
"strand": false,
"transcript": "ENST00000868857.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1132,
"aa_ref": "R",
"aa_start": 903,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3655,
"cdna_start": 2745,
"cds_end": null,
"cds_length": 3399,
"cds_start": 2707,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 23,
"exon_rank_end": null,
"feature": "ENST00000949199.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2707C>T",
"hgvs_p": "p.Arg903Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619258.1",
"strand": false,
"transcript": "ENST00000949199.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 1128,
"aa_ref": "R",
"aa_start": 950,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3650,
"cdna_start": 2892,
"cds_end": null,
"cds_length": 3387,
"cds_start": 2848,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "NM_001425072.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2848C>T",
"hgvs_p": "p.Arg950Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001412001.1",
"strand": false,
"transcript": "NM_001425072.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1153,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3725,
"cdna_start": null,
"cds_end": null,
"cds_length": 3462,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001425071.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2835-1374C>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001412000.1",
"strand": false,
"transcript": "NM_001425071.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1153,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3730,
"cdna_start": null,
"cds_end": null,
"cds_length": 3462,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000868855.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.2835-1374C>T",
"hgvs_p": null,
"intron_rank": 23,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000538914.1",
"strand": false,
"transcript": "ENST00000868855.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 137,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 416,
"cdna_start": null,
"cds_end": null,
"cds_length": 415,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000574026.2",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "c.339-1374C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467977.1",
"strand": false,
"transcript": "ENST00000574026.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 398,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000575043.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000262358",
"hgvs_c": "n.182G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000575043.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1004,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000571185.1",
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"hgvs_c": "n.406-1374C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000571185.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1716",
"effect": "missense_variant",
"frequency_reference_population": 0.32844782,
"gene_hgnc_id": 6147,
"gene_symbol": "ITGAE",
"gnomad_exomes_ac": 482335,
"gnomad_exomes_af": 0.335519,
"gnomad_exomes_homalt": 85299,
"gnomad_genomes_ac": 39361,
"gnomad_genomes_af": 0.261035,
"gnomad_genomes_homalt": 6309,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 91608,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.158,
"pos": 3729542,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.048,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.23000000417232513,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.23,
"transcript": "NM_002208.5"
}
]
}