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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: 22-17872017-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=17872017&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 17872017,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000441493.7",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val",
"transcript": "NM_015241.3",
"protein_id": "NP_056056.2",
"transcript_support_level": null,
"aa_start": 750,
"aa_end": null,
"aa_length": 2002,
"cds_start": 2248,
"cds_end": null,
"cds_length": 6009,
"cdna_start": 2603,
"cdna_end": null,
"cdna_length": 9447,
"mane_select": "ENST00000441493.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val",
"transcript": "ENST00000441493.7",
"protein_id": "ENSP00000416015.2",
"transcript_support_level": 5,
"aa_start": 750,
"aa_end": null,
"aa_length": 2002,
"cds_start": 2248,
"cds_end": null,
"cds_length": 6009,
"cdna_start": 2603,
"cdna_end": null,
"cdna_length": 9447,
"mane_select": "NM_015241.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2620A>G",
"hgvs_p": "p.Met874Val",
"transcript": "ENST00000585038.1",
"protein_id": "ENSP00000462033.1",
"transcript_support_level": 1,
"aa_start": 874,
"aa_end": null,
"aa_length": 1073,
"cds_start": 2620,
"cds_end": null,
"cds_length": 3222,
"cdna_start": 2682,
"cdna_end": null,
"cdna_length": 3323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val",
"transcript": "ENST00000400561.6",
"protein_id": "ENSP00000383406.2",
"transcript_support_level": 1,
"aa_start": 750,
"aa_end": null,
"aa_length": 966,
"cds_start": 2248,
"cds_end": null,
"cds_length": 2901,
"cdna_start": 2271,
"cdna_end": null,
"cdna_length": 3046,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val",
"transcript": "ENST00000383094.7",
"protein_id": "ENSP00000372574.3",
"transcript_support_level": 1,
"aa_start": 750,
"aa_end": null,
"aa_length": 948,
"cds_start": 2248,
"cds_end": null,
"cds_length": 2847,
"cdna_start": 2263,
"cdna_end": null,
"cdna_length": 2963,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2620A>G",
"hgvs_p": "p.Met874Val",
"transcript": "NM_001136004.3",
"protein_id": "NP_001129476.1",
"transcript_support_level": null,
"aa_start": 874,
"aa_end": null,
"aa_length": 1073,
"cds_start": 2620,
"cds_end": null,
"cds_length": 3222,
"cdna_start": 2694,
"cdna_end": null,
"cdna_length": 7795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2332A>G",
"hgvs_p": "p.Met778Val",
"transcript": "ENST00000414725.6",
"protein_id": "ENSP00000391827.2",
"transcript_support_level": 5,
"aa_start": 778,
"aa_end": null,
"aa_length": 976,
"cds_start": 2332,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2332,
"cdna_end": null,
"cdna_length": 4756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val",
"transcript": "NM_001122731.2",
"protein_id": "NP_001116203.1",
"transcript_support_level": null,
"aa_start": 750,
"aa_end": null,
"aa_length": 966,
"cds_start": 2248,
"cds_end": null,
"cds_length": 2901,
"cdna_start": 2322,
"cdna_end": null,
"cdna_length": 3090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "c.886A>G",
"hgvs_p": "p.Met296Val",
"transcript": "ENST00000461307.5",
"protein_id": "ENSP00000462531.1",
"transcript_support_level": 5,
"aa_start": 296,
"aa_end": null,
"aa_length": 495,
"cds_start": 886,
"cds_end": null,
"cds_length": 1488,
"cdna_start": 888,
"cdna_end": null,
"cdna_length": 5981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.303A>G",
"hgvs_p": null,
"transcript": "ENST00000462645.1",
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.472A>G",
"hgvs_p": null,
"transcript": "ENST00000465886.1",
"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": 559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.*1139A>G",
"hgvs_p": null,
"transcript": "ENST00000495076.5",
"protein_id": "ENSP00000434678.1",
"transcript_support_level": 5,
"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": 5113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.455A>G",
"hgvs_p": null,
"transcript": "ENST00000498345.1",
"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": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.2248A>G",
"hgvs_p": null,
"transcript": "ENST00000672019.1",
"protein_id": "ENSP00000500702.1",
"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": 9535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"hgvs_c": "n.*1139A>G",
"hgvs_p": null,
"transcript": "ENST00000495076.5",
"protein_id": "ENSP00000434678.1",
"transcript_support_level": 5,
"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": 5113,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MICAL3",
"gene_hgnc_id": 24694,
"dbsnp": "rs5992128",
"frequency_reference_population": 0.000004828032,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000482803,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.024238258600234985,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.077,
"revel_prediction": "Benign",
"alphamissense_score": 0.0576,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.871,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000441493.7",
"gene_symbol": "MICAL3",
"hgnc_id": 24694,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2248A>G",
"hgvs_p": "p.Met750Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}