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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: 12-49041162-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49041162&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 49041162,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_003482.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.6608C>T",
"hgvs_p": "p.Thr2203Met",
"transcript": "NM_003482.4",
"protein_id": "NP_003473.3",
"transcript_support_level": null,
"aa_start": 2203,
"aa_end": null,
"aa_length": 5537,
"cds_start": 6608,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 7827,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "ENST00000301067.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.6608C>T",
"hgvs_p": "p.Thr2203Met",
"transcript": "ENST00000301067.12",
"protein_id": "ENSP00000301067.7",
"transcript_support_level": 5,
"aa_start": 2203,
"aa_end": null,
"aa_length": 5537,
"cds_start": 6608,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 7827,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "NM_003482.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.6608C>T",
"hgvs_p": "p.Thr2203Met",
"transcript": "ENST00000683543.2",
"protein_id": "ENSP00000506726.1",
"transcript_support_level": null,
"aa_start": 2203,
"aa_end": null,
"aa_length": 5553,
"cds_start": 6608,
"cds_end": null,
"cds_length": 16662,
"cdna_start": 7827,
"cdna_end": null,
"cdna_length": 20686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.6617C>T",
"hgvs_p": "p.Thr2206Met",
"transcript": "ENST00000685166.1",
"protein_id": "ENSP00000509386.1",
"transcript_support_level": null,
"aa_start": 2206,
"aa_end": null,
"aa_length": 5540,
"cds_start": 6617,
"cds_end": null,
"cds_length": 16623,
"cdna_start": 6617,
"cdna_end": null,
"cdna_length": 16623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.6605C>T",
"hgvs_p": "p.Thr2202Met",
"transcript": "ENST00000692637.1",
"protein_id": "ENSP00000509666.1",
"transcript_support_level": null,
"aa_start": 2202,
"aa_end": null,
"aa_length": 5536,
"cds_start": 6605,
"cds_end": null,
"cds_length": 16611,
"cdna_start": 6605,
"cdna_end": null,
"cdna_length": 16611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.716C>T",
"hgvs_p": "p.Thr239Met",
"transcript": "ENST00000689944.1",
"protein_id": "ENSP00000508812.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 823,
"cds_start": 716,
"cds_end": null,
"cds_length": 2474,
"cdna_start": 717,
"cdna_end": null,
"cdna_length": 2475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.626C>T",
"hgvs_p": "p.Thr209Met",
"transcript": "ENST00000689060.1",
"protein_id": "ENSP00000509018.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 793,
"cds_start": 626,
"cds_end": null,
"cds_length": 2384,
"cdna_start": 627,
"cdna_end": null,
"cdna_length": 2385,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.281C>T",
"hgvs_p": null,
"transcript": "ENST00000689143.1",
"protein_id": "ENSP00000509839.1",
"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": 3958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"dbsnp": "rs770692765",
"frequency_reference_population": 0.000035495024,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000365149,
"gnomad_genomes_af": 0.0000263096,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2614623010158539,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.32,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0988,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.309,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003482.4",
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.6608C>T",
"hgvs_p": "p.Thr2203Met"
}
],
"clinvar_disease": "Kabuki syndrome,Kabuki syndrome 1,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:1",
"phenotype_combined": "Kabuki syndrome 1|Kabuki syndrome|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}