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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: 3-57073783-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=57073783&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 57073783,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_181727.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA12",
"gene_hgnc_id": 23221,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Asp",
"transcript": "NM_181727.2",
"protein_id": "NP_859078.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 190,
"cds_start": 89,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000334325.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_181727.2"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA12",
"gene_hgnc_id": 23221,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Asp",
"transcript": "ENST00000334325.2",
"protein_id": "ENSP00000335392.1",
"transcript_support_level": 1,
"aa_start": 30,
"aa_end": null,
"aa_length": 190,
"cds_start": 89,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_181727.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000334325.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+5443A>T",
"hgvs_p": null,
"transcript": "ENST00000338458.8",
"protein_id": "ENSP00000341071.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338458.8"
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA12",
"gene_hgnc_id": 23221,
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Asp",
"transcript": "ENST00000867038.1",
"protein_id": "ENSP00000537097.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 190,
"cds_start": 89,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867038.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+5443A>T",
"hgvs_p": null,
"transcript": "NM_001128615.2",
"protein_id": "NP_001122087.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128615.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+4764A>T",
"hgvs_p": null,
"transcript": "NM_001377407.1",
"protein_id": "NP_001364336.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377407.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-243+2963A>T",
"hgvs_p": null,
"transcript": "NM_001377408.1",
"protein_id": "NP_001364337.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 538,
"cds_start": null,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377408.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-243+5443A>T",
"hgvs_p": null,
"transcript": "NM_001377409.1",
"protein_id": "NP_001364338.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 538,
"cds_start": null,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377409.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-154+5443A>T",
"hgvs_p": null,
"transcript": "NM_001377410.1",
"protein_id": "NP_001364339.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 538,
"cds_start": null,
"cds_end": null,
"cds_length": 1617,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377410.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-32+5443A>T",
"hgvs_p": null,
"transcript": "NM_001377411.1",
"protein_id": "NP_001364340.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 527,
"cds_start": null,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377411.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-32+4764A>T",
"hgvs_p": null,
"transcript": "NM_001377412.1",
"protein_id": "NP_001364341.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 527,
"cds_start": null,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377412.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-32+5443A>T",
"hgvs_p": null,
"transcript": "ENST00000468727.5",
"protein_id": "ENSP00000417087.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 183,
"cds_start": null,
"cds_end": null,
"cds_length": 553,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468727.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+2963A>T",
"hgvs_p": null,
"transcript": "ENST00000468466.1",
"protein_id": "ENSP00000418469.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 99,
"cds_start": null,
"cds_end": null,
"cds_length": 300,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468466.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+2963A>T",
"hgvs_p": null,
"transcript": "XM_047448223.1",
"protein_id": "XP_047304179.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448223.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+2963A>T",
"hgvs_p": null,
"transcript": "XM_047448224.1",
"protein_id": "XP_047304180.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448224.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+5443A>T",
"hgvs_p": null,
"transcript": "XM_017006503.2",
"protein_id": "XP_016861992.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 483,
"cds_start": null,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006503.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "c.-28+4764A>T",
"hgvs_p": null,
"transcript": "XM_047448226.1",
"protein_id": "XP_047304182.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 483,
"cds_start": null,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448226.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "n.269+4764A>T",
"hgvs_p": null,
"transcript": "ENST00000477440.6",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000477440.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ARHGEF3",
"gene_hgnc_id": 683,
"hgvs_c": "n.-28+5443A>T",
"hgvs_p": null,
"transcript": "ENST00000477833.5",
"protein_id": "ENSP00000418984.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000477833.5"
}
],
"gene_symbol": "SPATA12",
"gene_hgnc_id": 23221,
"dbsnp": "rs748009888",
"frequency_reference_population": 0.000006156397,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.0000061564,
"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": 0.2211775779724121,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.158,
"revel_prediction": "Benign",
"alphamissense_score": 0.4332,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.509,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_181727.2",
"gene_symbol": "SPATA12",
"hgnc_id": 23221,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.89T>A",
"hgvs_p": "p.Val30Asp"
},
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001128615.2",
"gene_symbol": "ARHGEF3",
"hgnc_id": 683,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-28+5443A>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
}