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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: 12-49024662-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49024662&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 49024662,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000301067.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.15968G>A",
"hgvs_p": "p.Arg5323His",
"transcript": "NM_003482.4",
"protein_id": "NP_003473.3",
"transcript_support_level": null,
"aa_start": 5323,
"aa_end": null,
"aa_length": 5537,
"cds_start": 15968,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 17187,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "ENST00000301067.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 55,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.15968G>A",
"hgvs_p": "p.Arg5323His",
"transcript": "ENST00000301067.12",
"protein_id": "ENSP00000301067.7",
"transcript_support_level": 5,
"aa_start": 5323,
"aa_end": null,
"aa_length": 5537,
"cds_start": 15968,
"cds_end": null,
"cds_length": 16614,
"cdna_start": 17187,
"cdna_end": null,
"cdna_length": 20635,
"mane_select": "NM_003482.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 56,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.15968G>A",
"hgvs_p": "p.Arg5323His",
"transcript": "ENST00000683543.2",
"protein_id": "ENSP00000506726.1",
"transcript_support_level": null,
"aa_start": 5323,
"aa_end": null,
"aa_length": 5553,
"cds_start": 15968,
"cds_end": null,
"cds_length": 16662,
"cdna_start": 17187,
"cdna_end": null,
"cdna_length": 20686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.15977G>A",
"hgvs_p": "p.Arg5326His",
"transcript": "ENST00000685166.1",
"protein_id": "ENSP00000509386.1",
"transcript_support_level": null,
"aa_start": 5326,
"aa_end": null,
"aa_length": 5540,
"cds_start": 15977,
"cds_end": null,
"cds_length": 16623,
"cdna_start": 15977,
"cdna_end": null,
"cdna_length": 16623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.15965G>A",
"hgvs_p": "p.Arg5322His",
"transcript": "ENST00000692637.1",
"protein_id": "ENSP00000509666.1",
"transcript_support_level": null,
"aa_start": 5322,
"aa_end": null,
"aa_length": 5536,
"cds_start": 15965,
"cds_end": null,
"cds_length": 16611,
"cdna_start": 15965,
"cdna_end": null,
"cdna_length": 16611,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "c.503G>A",
"hgvs_p": "p.Arg168His",
"transcript": "ENST00000684428.1",
"protein_id": "ENSP00000507433.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 321,
"cds_start": 503,
"cds_end": null,
"cds_length": 966,
"cdna_start": 503,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_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": "c.47G>A",
"hgvs_p": "p.Arg16His",
"transcript": "ENST00000691932.1",
"protein_id": "ENSP00000509037.1",
"transcript_support_level": null,
"aa_start": 16,
"aa_end": null,
"aa_length": 204,
"cds_start": 47,
"cds_end": null,
"cds_length": 615,
"cdna_start": 47,
"cdna_end": null,
"cdna_length": 3417,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.640G>A",
"hgvs_p": null,
"transcript": "ENST00000681974.1",
"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": 1344,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.1683G>A",
"hgvs_p": null,
"transcript": "ENST00000683863.1",
"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": 2115,
"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.503G>A",
"hgvs_p": null,
"transcript": "ENST00000684755.1",
"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": 968,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.1120G>A",
"hgvs_p": null,
"transcript": "ENST00000685024.1",
"protein_id": "ENSP00000509185.1",
"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": 4570,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.*145G>A",
"hgvs_p": null,
"transcript": "ENST00000688411.1",
"protein_id": "ENSP00000510146.1",
"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": 815,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.*145G>A",
"hgvs_p": null,
"transcript": "ENST00000688411.1",
"protein_id": "ENSP00000510146.1",
"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": 815,
"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": "KMT2D",
"gene_hgnc_id": 7133,
"hgvs_c": "n.-101G>A",
"hgvs_p": null,
"transcript": "ENST00000682693.1",
"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": 2341,
"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.*1086G>A",
"hgvs_p": null,
"transcript": "ENST00000691463.1",
"protein_id": "ENSP00000510624.1",
"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": 1307,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KMT2D",
"gene_hgnc_id": 7133,
"dbsnp": "rs745599611",
"frequency_reference_population": 0.00000805616,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000821059,
"gnomad_genomes_af": 0.00000657272,
"gnomad_exomes_ac": 12,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6418717503547668,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.426,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4241,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.171,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.06,
"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": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000301067.12",
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.15968G>A",
"hgvs_p": "p.Arg5323His"
}
],
"clinvar_disease": "Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome,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": "US:4 B:1",
"phenotype_combined": "Kabuki syndrome 1|not provided|Kabuki syndrome|Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome;Kabuki syndrome 1|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}