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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: 12-49029232-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49029232&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 49029232,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000301067.12",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.14080G>C",
"hgvs_p": "p.Glu4694Gln",
"transcript": "NM_003482.4",
"protein_id": "NP_003473.3",
"transcript_support_level": null,
"aa_start": 4694,
"aa_end": null,
"aa_length": 5537,
"cds_start": 14080,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 15299,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "ENST00000301067.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.14080G>C",
"hgvs_p": "p.Glu4694Gln",
"transcript": "ENST00000301067.12",
"protein_id": "ENSP00000301067.7",
"transcript_support_level": 5,
"aa_start": 4694,
"aa_end": null,
"aa_length": 5537,
"cds_start": 14080,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 15299,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "NM_003482.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.14080G>C",
"hgvs_p": "p.Glu4694Gln",
"transcript": "ENST00000683543.2",
"protein_id": "ENSP00000506726.1",
"transcript_support_level": null,
"aa_start": 4694,
"aa_end": null,
"aa_length": 5553,
"cds_start": 14080,
"cds_end": null,
"cds_length": 16662,
"cdna_start": 15299,
"cdna_end": null,
"cdna_length": 20686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.14089G>C",
"hgvs_p": "p.Glu4697Gln",
"transcript": "ENST00000685166.1",
"protein_id": "ENSP00000509386.1",
"transcript_support_level": null,
"aa_start": 4697,
"aa_end": null,
"aa_length": 5540,
"cds_start": 14089,
"cds_end": null,
"cds_length": 16623,
"cdna_start": 14089,
"cdna_end": null,
"cdna_length": 16623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.14077G>C",
"hgvs_p": "p.Glu4693Gln",
"transcript": "ENST00000692637.1",
"protein_id": "ENSP00000509666.1",
"transcript_support_level": null,
"aa_start": 4693,
"aa_end": null,
"aa_length": 5536,
"cds_start": 14077,
"cds_end": null,
"cds_length": 16611,
"cdna_start": 14077,
"cdna_end": null,
"cdna_length": 16611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.379G>C",
"hgvs_p": "p.Glu127Gln",
"transcript": "ENST00000691986.1",
"protein_id": "ENSP00000509196.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 182,
"cds_start": 379,
"cds_end": null,
"cds_length": 550,
"cdna_start": 379,
"cdna_end": null,
"cdna_length": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.343G>C",
"hgvs_p": "p.Glu115Gln",
"transcript": "ENST00000685979.1",
"protein_id": "ENSP00000508906.1",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 170,
"cds_start": 343,
"cds_end": null,
"cds_length": 514,
"cdna_start": 343,
"cdna_end": null,
"cdna_length": 514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.340G>C",
"hgvs_p": "p.Glu114Gln",
"transcript": "ENST00000686564.1",
"protein_id": "ENSP00000509290.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 169,
"cds_start": 340,
"cds_end": null,
"cds_length": 511,
"cdna_start": 340,
"cdna_end": null,
"cdna_length": 511,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.172G>C",
"hgvs_p": null,
"transcript": "ENST00000687241.1",
"protein_id": "ENSP00000509842.1",
"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": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.*177G>C",
"hgvs_p": null,
"transcript": "ENST00000552391.2",
"protein_id": null,
"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": 928,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"dbsnp": "rs587778483",
"frequency_reference_population": 0.00011485661,
"hom_count_reference_population": 1,
"allele_count_reference_population": 185,
"gnomad_exomes_af": 0.00011793,
"gnomad_genomes_af": 0.0000854094,
"gnomad_exomes_ac": 172,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.014107972383499146,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.419,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8583,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.975,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.07,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS1_Supporting",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000301067.12",
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.14080G>C",
"hgvs_p": "p.Glu4694Gln"
}
],
"clinvar_disease": "Kabuki syndrome,Kabuki syndrome 1,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 LB:1 B:2 O:1",
"phenotype_combined": "not specified|Kabuki syndrome 1|not provided|Kabuki syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}