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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: 12-8823319-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=8823319&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 8823319,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000299698.12",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "NM_144670.6",
"protein_id": "NP_653271.3",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1454,
"cds_start": 200,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 5127,
"mane_select": "ENST00000299698.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "ENST00000299698.12",
"protein_id": "ENSP00000299698.7",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 1454,
"cds_start": 200,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 5127,
"mane_select": "NM_144670.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "XM_011520566.3",
"protein_id": "XP_011518868.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1467,
"cds_start": 200,
"cds_end": null,
"cds_length": 4404,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 5166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "XM_011520567.3",
"protein_id": "XP_011518869.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1467,
"cds_start": 200,
"cds_end": null,
"cds_length": 4404,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 4885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "XM_017018869.2",
"protein_id": "XP_016874358.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1466,
"cds_start": 200,
"cds_end": null,
"cds_length": 4401,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 4882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "XM_017018870.2",
"protein_id": "XP_016874359.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1454,
"cds_start": 200,
"cds_end": null,
"cds_length": 4365,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 4846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val",
"transcript": "XM_047428387.1",
"protein_id": "XP_047284343.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 1453,
"cds_start": 200,
"cds_end": null,
"cds_length": 4362,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 5124,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "n.231A>T",
"hgvs_p": null,
"transcript": "XR_001748594.2",
"protein_id": null,
"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": 5443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "n.231A>T",
"hgvs_p": null,
"transcript": "XR_931275.2",
"protein_id": null,
"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": 5482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "A2ML1-AS1",
"gene_hgnc_id": 41022,
"hgvs_c": "n.286+7343T>A",
"hgvs_p": null,
"transcript": "ENST00000537288.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "A2ML1-AS1",
"gene_hgnc_id": 41022,
"hgvs_c": "n.645+7343T>A",
"hgvs_p": null,
"transcript": "NR_046715.1",
"protein_id": null,
"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": 819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"hgvs_c": "n.-194A>T",
"hgvs_p": null,
"transcript": "ENST00000537546.1",
"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": 560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "A2ML1",
"gene_hgnc_id": 23336,
"dbsnp": "rs190479708",
"frequency_reference_population": 0.00078987377,
"hom_count_reference_population": 24,
"allele_count_reference_population": 1275,
"gnomad_exomes_af": 0.00075998,
"gnomad_genomes_af": 0.00107681,
"gnomad_exomes_ac": 1111,
"gnomad_genomes_ac": 164,
"gnomad_exomes_homalt": 21,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0031451284885406494,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.116,
"revel_prediction": "Benign",
"alphamissense_score": 0.1574,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.708,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000299698.12",
"gene_symbol": "A2ML1",
"hgnc_id": 23336,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.200A>T",
"hgvs_p": "p.Glu67Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000537288.1",
"gene_symbol": "A2ML1-AS1",
"hgnc_id": 41022,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.286+7343T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}