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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: 8-42165083-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=42165083&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 42165083,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006803.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "NM_006803.4",
"protein_id": "NP_006794.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 418,
"cds_start": 596,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396926.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006803.4"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "ENST00000396926.8",
"protein_id": "ENSP00000380132.3",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 418,
"cds_start": 596,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006803.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396926.8"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "ENST00000518421.5",
"protein_id": "ENSP00000428787.1",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 418,
"cds_start": 596,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000518421.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.*327C>T",
"hgvs_p": null,
"transcript": "ENST00000517865.5",
"protein_id": "ENSP00000430200.1",
"transcript_support_level": 1,
"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": "ENST00000517865.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.596C>T",
"hgvs_p": null,
"transcript": "ENST00000530375.5",
"protein_id": "ENSP00000431918.1",
"transcript_support_level": 1,
"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": "ENST00000530375.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.*327C>T",
"hgvs_p": null,
"transcript": "ENST00000517865.5",
"protein_id": "ENSP00000430200.1",
"transcript_support_level": 1,
"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": "ENST00000517865.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "NM_001134296.2",
"protein_id": "NP_001127768.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 418,
"cds_start": 596,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001134296.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.458C>T",
"hgvs_p": "p.Thr153Ile",
"transcript": "ENST00000858465.1",
"protein_id": "ENSP00000528524.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 372,
"cds_start": 458,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858465.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.458C>T",
"hgvs_p": "p.Thr153Ile",
"transcript": "ENST00000913687.1",
"protein_id": "ENSP00000583746.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 372,
"cds_start": 458,
"cds_end": null,
"cds_length": 1119,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913687.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "ENST00000943124.1",
"protein_id": "ENSP00000613183.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 344,
"cds_start": 596,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943124.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "ENST00000913686.1",
"protein_id": "ENSP00000583745.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 304,
"cds_start": 596,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913686.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.251C>T",
"hgvs_p": "p.Thr84Ile",
"transcript": "ENST00000521280.5",
"protein_id": "ENSP00000430616.1",
"transcript_support_level": 5,
"aa_start": 84,
"aa_end": null,
"aa_length": 286,
"cds_start": 251,
"cds_end": null,
"cds_length": 862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000521280.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile",
"transcript": "ENST00000517922.5",
"protein_id": "ENSP00000429435.1",
"transcript_support_level": 2,
"aa_start": 199,
"aa_end": null,
"aa_length": 268,
"cds_start": 596,
"cds_end": null,
"cds_length": 807,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000517922.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.185C>T",
"hgvs_p": "p.Thr62Ile",
"transcript": "ENST00000517499.5",
"protein_id": "ENSP00000429037.1",
"transcript_support_level": 3,
"aa_start": 62,
"aa_end": null,
"aa_length": 131,
"cds_start": 185,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000517499.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "c.251C>T",
"hgvs_p": "p.Thr84Ile",
"transcript": "XM_047421275.1",
"protein_id": "XP_047277231.1",
"transcript_support_level": null,
"aa_start": 84,
"aa_end": null,
"aa_length": 303,
"cds_start": 251,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421275.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.363C>T",
"hgvs_p": null,
"transcript": "ENST00000521899.1",
"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": "retained_intron",
"feature": "ENST00000521899.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.601C>T",
"hgvs_p": null,
"transcript": "ENST00000523249.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000523249.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"hgvs_c": "n.78-2583C>T",
"hgvs_p": null,
"transcript": "ENST00000520685.1",
"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": "ENST00000520685.1"
}
],
"gene_symbol": "AP3M2",
"gene_hgnc_id": 570,
"dbsnp": "rs148764977",
"frequency_reference_population": 0.00013075913,
"hom_count_reference_population": 0,
"allele_count_reference_population": 211,
"gnomad_exomes_af": 0.000127948,
"gnomad_genomes_af": 0.00015777,
"gnomad_exomes_ac": 187,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0853930115699768,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.203,
"revel_prediction": "Benign",
"alphamissense_score": 0.2301,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.104,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_006803.4",
"gene_symbol": "AP3M2",
"hgnc_id": 570,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.596C>T",
"hgvs_p": "p.Thr199Ile"
}
],
"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
}