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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: 12-49034855-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49034855&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 49034855,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000301067.12",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.10312G>A",
"hgvs_p": "p.Val3438Met",
"transcript": "NM_003482.4",
"protein_id": "NP_003473.3",
"transcript_support_level": null,
"aa_start": 3438,
"aa_end": null,
"aa_length": 5537,
"cds_start": 10312,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 11531,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "ENST00000301067.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.10312G>A",
"hgvs_p": "p.Val3438Met",
"transcript": "ENST00000301067.12",
"protein_id": "ENSP00000301067.7",
"transcript_support_level": 5,
"aa_start": 3438,
"aa_end": null,
"aa_length": 5537,
"cds_start": 10312,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 11531,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "NM_003482.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.10312G>A",
"hgvs_p": "p.Val3438Met",
"transcript": "ENST00000683543.2",
"protein_id": "ENSP00000506726.1",
"transcript_support_level": null,
"aa_start": 3438,
"aa_end": null,
"aa_length": 5553,
"cds_start": 10312,
"cds_end": null,
"cds_length": 16662,
"cdna_start": 11531,
"cdna_end": null,
"cdna_length": 20686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.10321G>A",
"hgvs_p": "p.Val3441Met",
"transcript": "ENST00000685166.1",
"protein_id": "ENSP00000509386.1",
"transcript_support_level": null,
"aa_start": 3441,
"aa_end": null,
"aa_length": 5540,
"cds_start": 10321,
"cds_end": null,
"cds_length": 16623,
"cdna_start": 10321,
"cdna_end": null,
"cdna_length": 16623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.10309G>A",
"hgvs_p": "p.Val3437Met",
"transcript": "ENST00000692637.1",
"protein_id": "ENSP00000509666.1",
"transcript_support_level": null,
"aa_start": 3437,
"aa_end": null,
"aa_length": 5536,
"cds_start": 10309,
"cds_end": null,
"cds_length": 16611,
"cdna_start": 10309,
"cdna_end": null,
"cdna_length": 16611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.1876G>A",
"hgvs_p": "p.Val626Met",
"transcript": "ENST00000687201.1",
"protein_id": "ENSP00000510037.1",
"transcript_support_level": null,
"aa_start": 626,
"aa_end": null,
"aa_length": 1256,
"cds_start": 1876,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 1876,
"cdna_end": null,
"cdna_length": 3771,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.*1761G>A",
"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
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.1876G>A",
"hgvs_p": null,
"transcript": "ENST00000692841.1",
"protein_id": "ENSP00000508711.1",
"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": 5009,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.*1761G>A",
"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": "rs35087111",
"frequency_reference_population": 0.00008240815,
"hom_count_reference_population": 0,
"allele_count_reference_population": 133,
"gnomad_exomes_af": 0.0000875693,
"gnomad_genomes_af": 0.0000328476,
"gnomad_exomes_ac": 128,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8182194232940674,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.588,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9787,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.855,
"phylop100way_prediction": "Pathogenic",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BP6,BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000301067.12",
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.10312G>A",
"hgvs_p": "p.Val3438Met"
}
],
"clinvar_disease": "Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome,Kabuki syndrome,Kabuki syndrome 1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 B:1",
"phenotype_combined": "Kabuki syndrome 1|Kabuki syndrome|Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome;Kabuki syndrome 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}