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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: 12-49038797-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49038797&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"hgvs_c": "c.8559G>A",
"hgvs_p": "p.Pro2853Pro",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_003482.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 456,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.8,
"chr": "12",
"clinvar_classification": "Likely benign",
"clinvar_disease": "KMT2D-related disorder,Kabuki syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 5537,
"aa_ref": "P",
"aa_start": 2853,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 20635,
"cdna_start": 9778,
"cds_end": null,
"cds_length": 16614,
"cds_start": 8559,
"consequences": [
"synonymous_variant"
],
"exon_count": 55,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "NM_003482.4",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.8559G>A",
"hgvs_p": "p.Pro2853Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000301067.12",
"protein_coding": true,
"protein_id": "NP_003473.3",
"strand": false,
"transcript": "NM_003482.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 5537,
"aa_ref": "P",
"aa_start": 2853,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 20635,
"cdna_start": 9778,
"cds_end": null,
"cds_length": 16614,
"cds_start": 8559,
"consequences": [
"synonymous_variant"
],
"exon_count": 55,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000301067.12",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.8559G>A",
"hgvs_p": "p.Pro2853Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003482.4",
"protein_coding": true,
"protein_id": "ENSP00000301067.7",
"strand": false,
"transcript": "ENST00000301067.12",
"transcript_support_level": 5
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 5553,
"aa_ref": "P",
"aa_start": 2853,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 20686,
"cdna_start": 9778,
"cds_end": null,
"cds_length": 16662,
"cds_start": 8559,
"consequences": [
"synonymous_variant"
],
"exon_count": 56,
"exon_rank": 35,
"exon_rank_end": null,
"feature": "ENST00000683543.2",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.8559G>A",
"hgvs_p": "p.Pro2853Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000506726.1",
"strand": false,
"transcript": "ENST00000683543.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 5540,
"aa_ref": "P",
"aa_start": 2856,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16623,
"cdna_start": 8568,
"cds_end": null,
"cds_length": 16623,
"cds_start": 8568,
"consequences": [
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000685166.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.8568G>A",
"hgvs_p": "p.Pro2856Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509386.1",
"strand": false,
"transcript": "ENST00000685166.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 5536,
"aa_ref": "P",
"aa_start": 2852,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16611,
"cdna_start": 8556,
"cds_end": null,
"cds_length": 16611,
"cds_start": 8556,
"consequences": [
"synonymous_variant"
],
"exon_count": 54,
"exon_rank": 34,
"exon_rank_end": null,
"feature": "ENST00000692637.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.8556G>A",
"hgvs_p": "p.Pro2852Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509666.1",
"strand": false,
"transcript": "ENST00000692637.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1256,
"aa_ref": "P",
"aa_start": 41,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3771,
"cdna_start": 123,
"cds_end": null,
"cds_length": 3771,
"cds_start": 123,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000687201.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.123G>A",
"hgvs_p": "p.Pro41Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510037.1",
"strand": false,
"transcript": "ENST00000687201.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2444,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000683043.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "n.258G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000683043.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3958,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000689143.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "n.*8G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509839.1",
"strand": false,
"transcript": "ENST00000689143.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5009,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000692841.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "n.123G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508711.1",
"strand": false,
"transcript": "ENST00000692841.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3958,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000689143.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "n.*8G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000509839.1",
"strand": false,
"transcript": "ENST00000689143.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs375344889",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0002876852,
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"gnomad_exomes_ac": 429,
"gnomad_exomes_af": 0.000299394,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 27,
"gnomad_genomes_af": 0.000177433,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified|Kabuki syndrome|KMT2D-related disorder|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.223,
"pos": 49038797,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003482.4"
}
]
}